rnalater  (Thermo Fisher)


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    Structured Review

    Thermo Fisher rnalater
    Augmented cell-mediated immune response in MDA-positive pigs vaccinated with mannose-conjugated and unconjugated CS NPs based influenza (mCS NPs-KAg and CS NPs-KAg) vaccines and not commercial flu vaccine. At day 6 post challenge infection with H1N1-OH7 virus the isolated MNCs of tracheobronchial lymph nodes (TBLN) were stimulated with vaccine virus (H1N2-OH10). (A) Lymphocytes proliferation stimulation index in TBLN was analyzed by ELISA. TBLN tissues stored in <t>RNAlater</t> were analyzed by qRT-PCR for the expression of mRNA of (B) IL-10; (C) IL-4; and (D) IFNγ. Data represent the mean value of three to four pigs ± SEM. Statistical analysis was carried out using one-way ANOVA followed by Tukey's post hoc comparison test. Asterisk refers to statistical difference between the two indicated groups (* p
    Rnalater, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Immunity and Protective Efficacy of Mannose Conjugated Chitosan-Based Influenza Nanovaccine in Maternal Antibody Positive Pigs"

    Article Title: Immunity and Protective Efficacy of Mannose Conjugated Chitosan-Based Influenza Nanovaccine in Maternal Antibody Positive Pigs

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2021.584299

    Augmented cell-mediated immune response in MDA-positive pigs vaccinated with mannose-conjugated and unconjugated CS NPs based influenza (mCS NPs-KAg and CS NPs-KAg) vaccines and not commercial flu vaccine. At day 6 post challenge infection with H1N1-OH7 virus the isolated MNCs of tracheobronchial lymph nodes (TBLN) were stimulated with vaccine virus (H1N2-OH10). (A) Lymphocytes proliferation stimulation index in TBLN was analyzed by ELISA. TBLN tissues stored in RNAlater were analyzed by qRT-PCR for the expression of mRNA of (B) IL-10; (C) IL-4; and (D) IFNγ. Data represent the mean value of three to four pigs ± SEM. Statistical analysis was carried out using one-way ANOVA followed by Tukey's post hoc comparison test. Asterisk refers to statistical difference between the two indicated groups (* p
    Figure Legend Snippet: Augmented cell-mediated immune response in MDA-positive pigs vaccinated with mannose-conjugated and unconjugated CS NPs based influenza (mCS NPs-KAg and CS NPs-KAg) vaccines and not commercial flu vaccine. At day 6 post challenge infection with H1N1-OH7 virus the isolated MNCs of tracheobronchial lymph nodes (TBLN) were stimulated with vaccine virus (H1N2-OH10). (A) Lymphocytes proliferation stimulation index in TBLN was analyzed by ELISA. TBLN tissues stored in RNAlater were analyzed by qRT-PCR for the expression of mRNA of (B) IL-10; (C) IL-4; and (D) IFNγ. Data represent the mean value of three to four pigs ± SEM. Statistical analysis was carried out using one-way ANOVA followed by Tukey's post hoc comparison test. Asterisk refers to statistical difference between the two indicated groups (* p

    Techniques Used: Multiple Displacement Amplification, Infection, Isolation, Enzyme-linked Immunosorbent Assay, Quantitative RT-PCR, Expressing

    2) Product Images from "Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes"

    Article Title: Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes

    Journal: bioRxiv

    doi: 10.1101/2021.07.20.453169

    Distribution of biochemical properties of identified proteins. A) molecular weight (kDa) B) isoelectric point C) number of predicted transmembrane helices. Bars represent the proportion (%) of identified proteins belonging in each range. E = ethanol; FF = flash-freezing; R = RNAlater; RF = RNAlater and flash-freezing; N = NAP buffer; AN = autoclaved NAP buffer.
    Figure Legend Snippet: Distribution of biochemical properties of identified proteins. A) molecular weight (kDa) B) isoelectric point C) number of predicted transmembrane helices. Bars represent the proportion (%) of identified proteins belonging in each range. E = ethanol; FF = flash-freezing; R = RNAlater; RF = RNAlater and flash-freezing; N = NAP buffer; AN = autoclaved NAP buffer.

    Techniques Used: Molecular Weight

    There were no significant differences in total numbers of PSMs, peptides, proteins, and protein groups between samples co-extracted after 1 week of preservation and only minimal differences existed in samples co-extracted after 4 weeks. FF = Flash-freezing, R = RNAlater, RF = RNAlater + flash freezing, N = NAP buffer, AN = Autoclaved NAP buffer, E = 95% Ethanol. 1 week = preserved for one week and first extraction batch. 4 weeks = preserved for 4 weeks and second extraction batch. Bars represent the arithmetic mean (n = 4 for all except E - 4 weeks where n = 3). Error bars represent standard deviation. Asterisks indicate statistical significance (t-test, p-value
    Figure Legend Snippet: There were no significant differences in total numbers of PSMs, peptides, proteins, and protein groups between samples co-extracted after 1 week of preservation and only minimal differences existed in samples co-extracted after 4 weeks. FF = Flash-freezing, R = RNAlater, RF = RNAlater + flash freezing, N = NAP buffer, AN = Autoclaved NAP buffer, E = 95% Ethanol. 1 week = preserved for one week and first extraction batch. 4 weeks = preserved for 4 weeks and second extraction batch. Bars represent the arithmetic mean (n = 4 for all except E - 4 weeks where n = 3). Error bars represent standard deviation. Asterisks indicate statistical significance (t-test, p-value

    Techniques Used: Preserving, Standard Deviation, T-Test

    3) Product Images from "A low-cost and easy-to-use cell preservation reagent for 4°C or room temperature sample storage"

    Article Title: A low-cost and easy-to-use cell preservation reagent for 4°C or room temperature sample storage

    Journal: bioRxiv

    doi: 10.1101/745232

    High quality RNA can be extracted from cells stored in a solution containing EDTA at 4°C for one week. A) Cartoon of protocol followed to preserved cells in solution. B) Representative 1% agarose gel with RNA from freshly harvested cells and compared with RNA from cells stored in RNAlater, PBS, PBS +, Tre +, and BSA +. Red arrows denote 28S, 18S, and 5S. C) Box plot depicting range of RNA concentrations, center bar indicates median. * denotes p
    Figure Legend Snippet: High quality RNA can be extracted from cells stored in a solution containing EDTA at 4°C for one week. A) Cartoon of protocol followed to preserved cells in solution. B) Representative 1% agarose gel with RNA from freshly harvested cells and compared with RNA from cells stored in RNAlater, PBS, PBS +, Tre +, and BSA +. Red arrows denote 28S, 18S, and 5S. C) Box plot depicting range of RNA concentrations, center bar indicates median. * denotes p

    Techniques Used: Agarose Gel Electrophoresis

    4) Product Images from "Robust Acquisition of Spatial Transcriptional Programs in Tissues With Immunofluorescence-Guided Laser Capture Microdissection"

    Article Title: Robust Acquisition of Spatial Transcriptional Programs in Tissues With Immunofluorescence-Guided Laser Capture Microdissection

    Journal: Frontiers in Cell and Developmental Biology

    doi: 10.3389/fcell.2022.853188

    Immuno-LCM-RNAseq of the human jejunum lymphatic vessel from a clinical, RNAlater-preserved jejunum tissue. (A) Left: Immunofluorescence image of the lymphatic vessels in the human jejunum tissue section using an anti-Podoplanin antibody (with 10 mM RVC). Right: bright field image after LCM. LC: lymphatic cells; Sm: submucosal layer; M: muscle layer (B) RNA quality of the leftover materials after LCM. (C) The quality of the cDNA library prepared from this RNA. Scale bar: 200 μm.
    Figure Legend Snippet: Immuno-LCM-RNAseq of the human jejunum lymphatic vessel from a clinical, RNAlater-preserved jejunum tissue. (A) Left: Immunofluorescence image of the lymphatic vessels in the human jejunum tissue section using an anti-Podoplanin antibody (with 10 mM RVC). Right: bright field image after LCM. LC: lymphatic cells; Sm: submucosal layer; M: muscle layer (B) RNA quality of the leftover materials after LCM. (C) The quality of the cDNA library prepared from this RNA. Scale bar: 200 μm.

    Techniques Used: Laser Capture Microdissection, Immunofluorescence, cDNA Library Assay

    5) Product Images from "Fine-tuned method to extract high purified proteins from the seagrass Halophila stipulacea to be used for proteome analyses"

    Article Title: Fine-tuned method to extract high purified proteins from the seagrass Halophila stipulacea to be used for proteome analyses

    Journal: bioRxiv

    doi: 10.1101/2021.07.23.453549

    SDS-PAGEs of purified proteins extracted from Halophila stipulacea plants frozen in liquid N 2 and following the Procedure 1, fixed in RNAlater and following the Procedure 2. Samples were loaded at different amount of 5, 10 and 20 µg for both extraction protocol.
    Figure Legend Snippet: SDS-PAGEs of purified proteins extracted from Halophila stipulacea plants frozen in liquid N 2 and following the Procedure 1, fixed in RNAlater and following the Procedure 2. Samples were loaded at different amount of 5, 10 and 20 µg for both extraction protocol.

    Techniques Used: Purification

    SDS-PAGEs of purified proteins extracted from Halophila stipulacea plants frozen in liquid N 2 and following the Procedure 2 or fixed in RNAlater and following the Procedure 1. Samples were loaded at different amount of 5, 10 and 20 µg for both extraction protocols. The white arrows indicate the marker bands that have been quantized by means of the Quantity One software. The black arrow indicates the major polypeptide appeared in the lane loaded with 5 µg proteins from the N 2 -Procedure 2 (see details in the text).
    Figure Legend Snippet: SDS-PAGEs of purified proteins extracted from Halophila stipulacea plants frozen in liquid N 2 and following the Procedure 2 or fixed in RNAlater and following the Procedure 1. Samples were loaded at different amount of 5, 10 and 20 µg for both extraction protocols. The white arrows indicate the marker bands that have been quantized by means of the Quantity One software. The black arrow indicates the major polypeptide appeared in the lane loaded with 5 µg proteins from the N 2 -Procedure 2 (see details in the text).

    Techniques Used: Purification, Marker, Software

    6) Product Images from "HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution"

    Article Title: HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

    Journal: Genome Biology and Evolution

    doi: 10.1093/gbe/evab112

    Statistical summary of locus recovery. ( A ) Plot representing the relationship between the minimal phylogenetic distance to a probe and three outcomes: the relative sequencing depth, the number of BWA-MEM mapped loci, and the number of BWA-ALN mapped loci. In each plot, fresh samples are shown in black, fresh samples also used for probes in green, and samples from museums with an age > 30 years in orange. Correlations were tested with Spearman’s correlation tests on fresh samples in black, museum samples in orange, and combined fresh and museum samples in gray. ( B ) Plots representing the relation between the age of the sample and the three previous outcomes. ( C ) Boxplots comparing the three previous outcomes between the museum samples and the fresh samples (including fresh samples also used for probes). Significance was evaluated using Wilcoxon rank tests. For the fresh samples additional boxplots show variation according to the sample storage history: 1) in absolute ethanol at room temperature, 2) in absolute ethanol at −20 °C, 3) dry at −80 °C, and 4) in RNAlater at −80 °C.
    Figure Legend Snippet: Statistical summary of locus recovery. ( A ) Plot representing the relationship between the minimal phylogenetic distance to a probe and three outcomes: the relative sequencing depth, the number of BWA-MEM mapped loci, and the number of BWA-ALN mapped loci. In each plot, fresh samples are shown in black, fresh samples also used for probes in green, and samples from museums with an age > 30 years in orange. Correlations were tested with Spearman’s correlation tests on fresh samples in black, museum samples in orange, and combined fresh and museum samples in gray. ( B ) Plots representing the relation between the age of the sample and the three previous outcomes. ( C ) Boxplots comparing the three previous outcomes between the museum samples and the fresh samples (including fresh samples also used for probes). Significance was evaluated using Wilcoxon rank tests. For the fresh samples additional boxplots show variation according to the sample storage history: 1) in absolute ethanol at room temperature, 2) in absolute ethanol at −20 °C, 3) dry at −80 °C, and 4) in RNAlater at −80 °C.

    Techniques Used: Sequencing

    7) Product Images from "Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota"

    Article Title: Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

    Journal: PeerJ

    doi: 10.7717/peerj.4827

    Relative abundances of 24 highest taxonomic classifications of bacteria over 56 days. Each column represents the average of samples collected on Day 0, 7, 14, and 56 at (A) 25 °C, (B) 4 °C, and (C) −80 °C. Canine fecal microbiota was largely dominated by genera Prevotella and Streptococccus . Comparison of Day 0 samples in different preservation buffers revealed rapid changes in abundance of Prevotella and Streptococcus with 70% ethanol and RNAlater. *Time points were excluded from samples that did not pass sequencing quality or low abundance OTU filtering.
    Figure Legend Snippet: Relative abundances of 24 highest taxonomic classifications of bacteria over 56 days. Each column represents the average of samples collected on Day 0, 7, 14, and 56 at (A) 25 °C, (B) 4 °C, and (C) −80 °C. Canine fecal microbiota was largely dominated by genera Prevotella and Streptococccus . Comparison of Day 0 samples in different preservation buffers revealed rapid changes in abundance of Prevotella and Streptococcus with 70% ethanol and RNAlater. *Time points were excluded from samples that did not pass sequencing quality or low abundance OTU filtering.

    Techniques Used: Preserving, Sequencing

    8) Product Images from "Molecular detection and quantification of Plasmodium falciparum-infected human hepatocytes in chimeric immune-deficient mice"

    Article Title: Molecular detection and quantification of Plasmodium falciparum-infected human hepatocytes in chimeric immune-deficient mice

    Journal: Malaria Journal

    doi: 10.1186/1475-2875-12-430

    Standardizing the sampling of humanized liver fragments. Five days post-infection, mice are euthanized by cervical dislocation. The livers are carefully removed, rinsed in PBS and 12 standardized fragments (A-L) are prepared and placed in RNALater until further analysis.
    Figure Legend Snippet: Standardizing the sampling of humanized liver fragments. Five days post-infection, mice are euthanized by cervical dislocation. The livers are carefully removed, rinsed in PBS and 12 standardized fragments (A-L) are prepared and placed in RNALater until further analysis.

    Techniques Used: Sampling, Infection, Mouse Assay

    9) Product Images from "Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions"

    Article Title: Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-35843-0

    Overview of storage conditions for each of the three separate donor feces. 45 fecal samples were obtained from each donor feces. The samples were processed in triplicates and either stored directly at −80 °C, at −20 °C for 24 or 72 hours, or in one of the following buffers: DNA/RNA Shield, PSP Buffer, or RNAlater at 4 °C/RT, prior to freezing at −80 °C. Red numbers indicate number of samples that progress to this storage methodology.
    Figure Legend Snippet: Overview of storage conditions for each of the three separate donor feces. 45 fecal samples were obtained from each donor feces. The samples were processed in triplicates and either stored directly at −80 °C, at −20 °C for 24 or 72 hours, or in one of the following buffers: DNA/RNA Shield, PSP Buffer, or RNAlater at 4 °C/RT, prior to freezing at −80 °C. Red numbers indicate number of samples that progress to this storage methodology.

    Techniques Used:

    10) Product Images from "L-arginine Supplementation Improves Responses to Injury and Inflammation in Dextran Sulfate Sodium Colitis"

    Article Title: L-arginine Supplementation Improves Responses to Injury and Inflammation in Dextran Sulfate Sodium Colitis

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0033546

    Tissue microarray assessment identifying multiple differentially expressed genes after exposure to DSS. Mice received treatments as in Figures 3 – 6 . There were four groups, namely control (Ctrl), receiving water alone; control+L-Arg, receiving water for 6 days and L-Arg for 4 days; DSS, receiving DSS for 6 days and water for 4 days; and DSS+L-Arg, receiving DSS for 6 days and L-Arg for 4 days. At sacrifice, a piece of colon was obtained and placed in RNAlater®. Three samples from each of the four groups were submitted for microarray assessment. (A) Hierarchical clustering of the samples based on > 16,000 protein-coding genes. The 12 samples were clustered by the expression values of the probes to examine the inter- and intra-groups relationship of the samples. Note that the DSS group was markedly distinct from the Ctrl or the Ctrl+L-Arg groups, and the DSS+L-Arg group segregated closely with the control groups not receiving DSS, rather than with the DSS group. (B) Table of the number of differentially expressed genes (DEGs) based on p value
    Figure Legend Snippet: Tissue microarray assessment identifying multiple differentially expressed genes after exposure to DSS. Mice received treatments as in Figures 3 – 6 . There were four groups, namely control (Ctrl), receiving water alone; control+L-Arg, receiving water for 6 days and L-Arg for 4 days; DSS, receiving DSS for 6 days and water for 4 days; and DSS+L-Arg, receiving DSS for 6 days and L-Arg for 4 days. At sacrifice, a piece of colon was obtained and placed in RNAlater®. Three samples from each of the four groups were submitted for microarray assessment. (A) Hierarchical clustering of the samples based on > 16,000 protein-coding genes. The 12 samples were clustered by the expression values of the probes to examine the inter- and intra-groups relationship of the samples. Note that the DSS group was markedly distinct from the Ctrl or the Ctrl+L-Arg groups, and the DSS+L-Arg group segregated closely with the control groups not receiving DSS, rather than with the DSS group. (B) Table of the number of differentially expressed genes (DEGs) based on p value

    Techniques Used: Microarray, Mouse Assay, Expressing

    11) Product Images from "A Minimally Invasive Method for Retrieving Single Adherent Cells of Different Types from Cultures"

    Article Title: A Minimally Invasive Method for Retrieving Single Adherent Cells of Different Types from Cultures

    Journal: Scientific Reports

    doi: 10.1038/srep05424

    Comparison of RNA preservation levels between medium, RNALater and RNA Lysis Buffer during single-cell harvesting. The quantification cycle (C q ) values are higher in the lysis buffer group for the 28S (Panel A) and higher in the RNALater group for the ACTB gene (Panel B) as compared with the medium group. The corresponding C q mean values are shown on top of the bars to compare the three conditions. Errors and error bars are corresponding standard deviations. The number of cells analyzed (n) for each harvesting condition is shown at the bottom of the graphs. Each qPCR reaction was run with three technical replicates. The difference between the lysis buffer and medium preservation group is statistically significant for the 28S gene and between the RNALater and medium group for the ACTB gene (both tested with the two-tailed Mann-Whitney test, α = 0.05). Therefore, dispensing cells in cell culture medium can better preserve mRNA.
    Figure Legend Snippet: Comparison of RNA preservation levels between medium, RNALater and RNA Lysis Buffer during single-cell harvesting. The quantification cycle (C q ) values are higher in the lysis buffer group for the 28S (Panel A) and higher in the RNALater group for the ACTB gene (Panel B) as compared with the medium group. The corresponding C q mean values are shown on top of the bars to compare the three conditions. Errors and error bars are corresponding standard deviations. The number of cells analyzed (n) for each harvesting condition is shown at the bottom of the graphs. Each qPCR reaction was run with three technical replicates. The difference between the lysis buffer and medium preservation group is statistically significant for the 28S gene and between the RNALater and medium group for the ACTB gene (both tested with the two-tailed Mann-Whitney test, α = 0.05). Therefore, dispensing cells in cell culture medium can better preserve mRNA.

    Techniques Used: Preserving, Lysis, Cell Harvesting, Real-time Polymerase Chain Reaction, Two Tailed Test, MANN-WHITNEY, Cell Culture

    12) Product Images from "Pancreatic Ductal Adenocarcinoma (PDAC) circulating tumor cells influence myeloid cell differentiation to support their survival and immunoresistance in portal vein circulation"

    Article Title: Pancreatic Ductal Adenocarcinoma (PDAC) circulating tumor cells influence myeloid cell differentiation to support their survival and immunoresistance in portal vein circulation

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0265725

    RNA expression of myeloid growth factor signaling ligands and their receptors in uncultured PDAC CTC and M-FB isolated cells and in vivo formed clusters. Uncultured portal blood CTC, M-FB, and in vivo formed CTC+/M-FB+ clusters from PortalBMC of 6 PDAC patients were FACS isolated and collected into RNALater, and then extracted and analyzed for CSF2 , CSF1 , IL34 , CSF1R , and CSF2R RNA expression by real-time RT-PCR. ( A ) CSF1 (M-CSF) RNA expression was elevated in isolated CTC and CSF2 (GM-CSF) RNA expression was elevated in vivo CTC+M-FB clusters. High variability was seen in isolated CTC CSF1 RNA expression, complicating interpretation of statistical analyses. CSF2 expression was higher in in vivo clusters compared to CTC alone (p = 0.0322). Though found elevated in both, IL34 RNA expression was higher in isolated CTC than in in vivo clusters (p = 0.0186). ( B ) M-CSF/IL-34 receptor CSF1R mRNA expression was detectable in CTC, in vivo clusters, and M-FB, with the expression highest but most variable in M-FB. CSF2R RNA expression was not detected in this sample set. Due to limitations in uncultured cell isolate numbers, RNA for CXCL8 (IL8) and CXCR2 were not analyzed. Bars depict mean of values and error bars indicate standard error from the mean.
    Figure Legend Snippet: RNA expression of myeloid growth factor signaling ligands and their receptors in uncultured PDAC CTC and M-FB isolated cells and in vivo formed clusters. Uncultured portal blood CTC, M-FB, and in vivo formed CTC+/M-FB+ clusters from PortalBMC of 6 PDAC patients were FACS isolated and collected into RNALater, and then extracted and analyzed for CSF2 , CSF1 , IL34 , CSF1R , and CSF2R RNA expression by real-time RT-PCR. ( A ) CSF1 (M-CSF) RNA expression was elevated in isolated CTC and CSF2 (GM-CSF) RNA expression was elevated in vivo CTC+M-FB clusters. High variability was seen in isolated CTC CSF1 RNA expression, complicating interpretation of statistical analyses. CSF2 expression was higher in in vivo clusters compared to CTC alone (p = 0.0322). Though found elevated in both, IL34 RNA expression was higher in isolated CTC than in in vivo clusters (p = 0.0186). ( B ) M-CSF/IL-34 receptor CSF1R mRNA expression was detectable in CTC, in vivo clusters, and M-FB, with the expression highest but most variable in M-FB. CSF2R RNA expression was not detected in this sample set. Due to limitations in uncultured cell isolate numbers, RNA for CXCL8 (IL8) and CXCR2 were not analyzed. Bars depict mean of values and error bars indicate standard error from the mean.

    Techniques Used: RNA Expression, Isolation, In Vivo, FACS, Quantitative RT-PCR, Expressing

    13) Product Images from "A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery"

    Article Title: A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery

    Journal: Virology

    doi: 10.1016/j.virol.2018.12.020

    Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBSplit to the appropriate reference sequence, 16S bacterial rRNA (A), 23S bacterial rRNA (B), Elizabethkingia anophelis transcriptome (C and D) and the NCBI bacterial genome database (E). The reads called for each gene was determined using BBMap with output flag rpkm (D). All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.
    Figure Legend Snippet: Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBSplit to the appropriate reference sequence, 16S bacterial rRNA (A), 23S bacterial rRNA (B), Elizabethkingia anophelis transcriptome (C and D) and the NCBI bacterial genome database (E). The reads called for each gene was determined using BBMap with output flag rpkm (D). All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.

    Techniques Used: Purification, Sequencing

    Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBMap or BBSplit to the appropriate reference sequence, An. gambiae transcriptome (A and B), West Nile virus (C) or Bolahun virus (D). The reads called for each gene was determined using BBMap with output flag rpkm (B). Variants detected in Bolahun virus were called using LoFreq (F). Only variants present at greater than 5% were used for analysis. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.
    Figure Legend Snippet: Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBMap or BBSplit to the appropriate reference sequence, An. gambiae transcriptome (A and B), West Nile virus (C) or Bolahun virus (D). The reads called for each gene was determined using BBMap with output flag rpkm (B). Variants detected in Bolahun virus were called using LoFreq (F). Only variants present at greater than 5% were used for analysis. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.

    Techniques Used: Purification, Sequencing

    Reverse Transcriptase mediated ribosomal RNA (rRNA) depletion increases target-specific coverage while reducing the number of rRNA reads in next-generation sequencing. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNase H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using BBSplit to the appropriate reference sequence, unique reads after duplicate removal (A), 18S rRNA (B), 28S rRNA (C) and mitochondrial 16S rRNA (D). Reads for 18S (E) and 28S (F) rRNA were then normalized to host gene AGAP001826-RA and then compared. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.
    Figure Legend Snippet: Reverse Transcriptase mediated ribosomal RNA (rRNA) depletion increases target-specific coverage while reducing the number of rRNA reads in next-generation sequencing. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNase H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using BBSplit to the appropriate reference sequence, unique reads after duplicate removal (A), 18S rRNA (B), 28S rRNA (C) and mitochondrial 16S rRNA (D). Reads for 18S (E) and 28S (F) rRNA were then normalized to host gene AGAP001826-RA and then compared. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.

    Techniques Used: Next-Generation Sequencing, Purification, Sequencing

    14) Product Images from "A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery"

    Article Title: A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery

    Journal: Virology

    doi: 10.1016/j.virol.2018.12.020

    Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBSplit to the appropriate reference sequence, 16S bacterial rRNA (A), 23S bacterial rRNA (B), Elizabethkingia anophelis transcriptome (C and D) and the NCBI bacterial genome database (E). The reads called for each gene was determined using BBMap with output flag rpkm (D). All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.
    Figure Legend Snippet: Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBSplit to the appropriate reference sequence, 16S bacterial rRNA (A), 23S bacterial rRNA (B), Elizabethkingia anophelis transcriptome (C and D) and the NCBI bacterial genome database (E). The reads called for each gene was determined using BBMap with output flag rpkm (D). All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.

    Techniques Used: Purification, Sequencing

    Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBMap or BBSplit to the appropriate reference sequence, An. gambiae transcriptome (A and B), West Nile virus (C) or Bolahun virus (D). The reads called for each gene was determined using BBMap with output flag rpkm (B). Variants detected in Bolahun virus were called using LoFreq (F). Only variants present at greater than 5% were used for analysis. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.
    Figure Legend Snippet: Percent of reads to bacterial rRNA and host transcripts are increased in depleted samples. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNAse H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using either BBMap or BBSplit to the appropriate reference sequence, An. gambiae transcriptome (A and B), West Nile virus (C) or Bolahun virus (D). The reads called for each gene was determined using BBMap with output flag rpkm (B). Variants detected in Bolahun virus were called using LoFreq (F). Only variants present at greater than 5% were used for analysis. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.

    Techniques Used: Purification, Sequencing

    Reverse Transcriptase mediated ribosomal RNA (rRNA) depletion increases target-specific coverage while reducing the number of rRNA reads in next-generation sequencing. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNase H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using BBSplit to the appropriate reference sequence, unique reads after duplicate removal (A), 18S rRNA (B), 28S rRNA (C) and mitochondrial 16S rRNA (D). Reads for 18S (E) and 28S (F) rRNA were then normalized to host gene AGAP001826-RA and then compared. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.
    Figure Legend Snippet: Reverse Transcriptase mediated ribosomal RNA (rRNA) depletion increases target-specific coverage while reducing the number of rRNA reads in next-generation sequencing. Anopheles gambiae mosquitoes were exposed to an infectious bloodmeal containing 10 7 PFU of West Nile virus strain NY99. The following day, midguts were dissected and the residual bloodmeal was spread onto a CloneSaver FTA card (GE Healthcare, USA) and then soaked in RNAlater solution to stabilize the nucleic acid and facilitate dispersion. Total nucleic acid was then extracted, and DNase treated. This is considered the input RNA. DNase-free RNA was then reverse transcribed using either ribosomal RNA specific probes (RT – with Probes) or without probes (RT – no Probes). The samples were then treated with RNase H and DNase I and purified. The samples were then subjected to library preparation and sequenced on an Illumina MiSeq. Reads were then demultiplexed and subsequently trimmed using BBDuk. Each sample was then normalized to contain 1.5 million reads to allow for direct comparisons. Duplicate reads were removed using Clumpify and then unique reads were mapped using BBSplit to the appropriate reference sequence, unique reads after duplicate removal (A), 18S rRNA (B), 28S rRNA (C) and mitochondrial 16S rRNA (D). Reads for 18S (E) and 28S (F) rRNA were then normalized to host gene AGAP001826-RA and then compared. All statistical tests were performed by One-Way ANOVA with Tukey test for multiple comparisons. The p-values are indicated as numbers. All p-values without an accompanying bar are statistical comparisons between the input RNA and the other group. The other comparisons with a bar are statistical comparisons between the two groups that are below the corresponding bar.

    Techniques Used: Next-Generation Sequencing, Purification, Sequencing

    15) Product Images from "Limitations of using feline coronavirus spike protein gene mutations to diagnose feline infectious peritonitis"

    Article Title: Limitations of using feline coronavirus spike protein gene mutations to diagnose feline infectious peritonitis

    Journal: Veterinary Research

    doi: 10.1186/s13567-017-0467-9

    Diagnostic pathway used. Asterisk: Cats for which no samples were collected into formalin or RNAlater were excluded from further analysis.
    Figure Legend Snippet: Diagnostic pathway used. Asterisk: Cats for which no samples were collected into formalin or RNAlater were excluded from further analysis.

    Techniques Used: Diagnostic Assay

    16) Product Images from "Calcium and Vitamin D increase mRNA levels for the growth control hIK1 channel in human epidermal keratinocytes but functional channels are not observed"

    Article Title: Calcium and Vitamin D increase mRNA levels for the growth control hIK1 channel in human epidermal keratinocytes but functional channels are not observed

    Journal: BMC Dermatology

    doi: 10.1186/1471-5945-4-7

    Consistent hIK1 mRNA levels among biopsies from individuals and donor groups are maintained in explant culture. Real-time PCR analysis of mRNA expression levels (normalized to GAPDH) in human skin biopsies from healthy donors. (a) data points are hIK1 mRNA levels from three biopsies from each of three donors with mRNA harvesting performed at time of biopsy collection. There were no statistically significance differences in hIK1 expression among the three donors. (b) effects of culture time on gene expression in explant biopsies assessed by measuring mRNA levels from biopsies preserved in RNALater at time of collection, and assessing fold changes from these levels in sibling biopsies shipped overnight in culture medium (1 day post collect), or shipped and kept in culture for 1 and 2 additional days (2 and 4 days post collect). Expression of involucrin (INV) and transglutaminase (TG-1) are shown for comparison with hIK1. Each data point is mean ± SEM for 3 biopsies. For any given gene there were no statistically significant differences in expression when comparing data from days one, two, and four.
    Figure Legend Snippet: Consistent hIK1 mRNA levels among biopsies from individuals and donor groups are maintained in explant culture. Real-time PCR analysis of mRNA expression levels (normalized to GAPDH) in human skin biopsies from healthy donors. (a) data points are hIK1 mRNA levels from three biopsies from each of three donors with mRNA harvesting performed at time of biopsy collection. There were no statistically significance differences in hIK1 expression among the three donors. (b) effects of culture time on gene expression in explant biopsies assessed by measuring mRNA levels from biopsies preserved in RNALater at time of collection, and assessing fold changes from these levels in sibling biopsies shipped overnight in culture medium (1 day post collect), or shipped and kept in culture for 1 and 2 additional days (2 and 4 days post collect). Expression of involucrin (INV) and transglutaminase (TG-1) are shown for comparison with hIK1. Each data point is mean ± SEM for 3 biopsies. For any given gene there were no statistically significant differences in expression when comparing data from days one, two, and four.

    Techniques Used: Real-time Polymerase Chain Reaction, Expressing

    17) Product Images from "Macrophage colony-stimulating factor (CSF1) controls monocyte production and maturation and the steady-state size of the liver in pigs"

    Article Title: Macrophage colony-stimulating factor (CSF1) controls monocyte production and maturation and the steady-state size of the liver in pigs

    Journal: American Journal of Physiology - Gastrointestinal and Liver Physiology

    doi: 10.1152/ajpgi.00116.2016

    Effect of CSF1-Fc on gene expression in the liver. Pigs (8-wk-old males and females) were injected with PBS or 0.75 mg/kg CSF1-Fc for 3 days prior to euthanasia on day 4 . Liver tissue was collected in RNAlater and RNA was prepared and submitted for microarray analysis. A : expression profiles of a number of genes from cluster 1 : upregulated genes in CSF1-Fc-treated pigs and a table of the top 12 enrichment clusters with representative terms. B : expression profiles of a number of genes from cluster 2 : downregulated genes in CSF1-Fc-treated pigs and a table of the top 12 enrichment clusters with representative terms. C : expression profiles of a number of genes that were unregulated.
    Figure Legend Snippet: Effect of CSF1-Fc on gene expression in the liver. Pigs (8-wk-old males and females) were injected with PBS or 0.75 mg/kg CSF1-Fc for 3 days prior to euthanasia on day 4 . Liver tissue was collected in RNAlater and RNA was prepared and submitted for microarray analysis. A : expression profiles of a number of genes from cluster 1 : upregulated genes in CSF1-Fc-treated pigs and a table of the top 12 enrichment clusters with representative terms. B : expression profiles of a number of genes from cluster 2 : downregulated genes in CSF1-Fc-treated pigs and a table of the top 12 enrichment clusters with representative terms. C : expression profiles of a number of genes that were unregulated.

    Techniques Used: Expressing, Injection, Microarray

    18) Product Images from "Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh"

    Article Title: Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.00361-17

    Mean technical reproducibility and 95% CIs from day 0 replicates (A) and day 4 replicates (B) for the relative abundance of three phyla, two alpha diversity metrics, and four beta diversity metrics by fecal sample collection method using intraclass correlation coefficients. For day 0, samples from 38, 36, 46, 42, and 47 individuals were included for no solution, FIT tube, FOBT card, RNAlater, and 95% ethanol samples, respectively. For day 4, samples from 41, 50, 43, and 46 individuals were included for FIT tube, FOBT card, RNAlater, and 95% ethanol samples, respectively. BC, Bray-Curtis distance.
    Figure Legend Snippet: Mean technical reproducibility and 95% CIs from day 0 replicates (A) and day 4 replicates (B) for the relative abundance of three phyla, two alpha diversity metrics, and four beta diversity metrics by fecal sample collection method using intraclass correlation coefficients. For day 0, samples from 38, 36, 46, 42, and 47 individuals were included for no solution, FIT tube, FOBT card, RNAlater, and 95% ethanol samples, respectively. For day 4, samples from 41, 50, 43, and 46 individuals were included for FIT tube, FOBT card, RNAlater, and 95% ethanol samples, respectively. BC, Bray-Curtis distance.

    Techniques Used:

    Mean stability and 95% CIs by fecal sample collection methods (i.e., day 4 fecal samples compared with day 0 fecal samples) for the relative abundance of three phyla, two alpha diversity metrics, and four beta diversity metrics using intraclass correlation coefficients. Samples from 47, 50, 48, and 49 individuals were included for the FIT tube, FOBT card, RNAlater, and 95% ethanol samples, respectively.
    Figure Legend Snippet: Mean stability and 95% CIs by fecal sample collection methods (i.e., day 4 fecal samples compared with day 0 fecal samples) for the relative abundance of three phyla, two alpha diversity metrics, and four beta diversity metrics using intraclass correlation coefficients. Samples from 47, 50, 48, and 49 individuals were included for the FIT tube, FOBT card, RNAlater, and 95% ethanol samples, respectively.

    Techniques Used:

    19) Product Images from "Identification of Eukaryotic Open Reading Frames in Metagenomic cDNA Libraries Made from Environmental Samples †"

    Article Title: Identification of Eukaryotic Open Reading Frames in Metagenomic cDNA Libraries Made from Environmental Samples †

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.72.1.135-143.2006

    Effect of storage in RNAlater on the stability of total RNA extracted from Acanthamoeba polyphaga . (A) TBE 1.2% agarose gel. Lane 1, RNA size markers (Millennium markers; Ambion); lanes 2 and 3, total RNA from a fresh culture of Acanthamoeba polyphaga. (B) Same as panel A, but lane 2, total RNA from A. polyphaga stored in RNAlater for 10 days at ambient temperature; lane 3, total RNA from A. polyphaga stored for 10 days at 4°C.
    Figure Legend Snippet: Effect of storage in RNAlater on the stability of total RNA extracted from Acanthamoeba polyphaga . (A) TBE 1.2% agarose gel. Lane 1, RNA size markers (Millennium markers; Ambion); lanes 2 and 3, total RNA from a fresh culture of Acanthamoeba polyphaga. (B) Same as panel A, but lane 2, total RNA from A. polyphaga stored in RNAlater for 10 days at ambient temperature; lane 3, total RNA from A. polyphaga stored for 10 days at 4°C.

    Techniques Used: Agarose Gel Electrophoresis

    20) Product Images from "Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota"

    Article Title: Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

    Journal: PeerJ

    doi: 10.7717/peerj.4827

    Relative abundances of 24 highest taxonomic classifications of bacteria over 56 days. Each column represents the average of samples collected on Day 0, 7, 14, and 56 at (A) 25 °C, (B) 4 °C, and (C) −80 °C. Canine fecal microbiota was largely dominated by genera Prevotella and Streptococccus . Comparison of Day 0 samples in different preservation buffers revealed rapid changes in abundance of Prevotella and Streptococcus with 70% ethanol and RNAlater. *Time points were excluded from samples that did not pass sequencing quality or low abundance OTU filtering.
    Figure Legend Snippet: Relative abundances of 24 highest taxonomic classifications of bacteria over 56 days. Each column represents the average of samples collected on Day 0, 7, 14, and 56 at (A) 25 °C, (B) 4 °C, and (C) −80 °C. Canine fecal microbiota was largely dominated by genera Prevotella and Streptococccus . Comparison of Day 0 samples in different preservation buffers revealed rapid changes in abundance of Prevotella and Streptococcus with 70% ethanol and RNAlater. *Time points were excluded from samples that did not pass sequencing quality or low abundance OTU filtering.

    Techniques Used: Preserving, Sequencing

    21) Product Images from "Tolerogenic bone marrow-derived dendritic cells induce neuroprotective regulatory T cells in a model of Parkinson’s disease"

    Article Title: Tolerogenic bone marrow-derived dendritic cells induce neuroprotective regulatory T cells in a model of Parkinson’s disease

    Journal: Molecular Neurodegeneration

    doi: 10.1186/s13024-018-0255-7

    Gene expression in midbrain after treatment with MPTP or BMDCs and MPTP. BMDCs were differentiated for 8 days in 20 ng/ml GM-CSF prior to 3 days of pretreatment in media alone. These BMDCs were transferred i.v. one and two weeks prior to intoxication with four doses of 16 mg/kg MPTP. Two days after intoxication, PBS, MPTP and BMDC + MPTP mice were sacrificed and the brain was removed, hemisected and the midbrain was incubated in RNAlater for 24 h prior to freezing at − 80 °C. RNA was isolated from the midbrain, converted to cDNA PCR arrays of proinflammatory genes were run. a Gene expression was determined relative to the PBS control midbrains; n = 3 for PBS and n = 4 for MPTP and MPTP+BMDCs. Fold change was determined using SA Bioscience software. b Ingenuity Pathway Analysis was used to determine the expression of genes associated with the inflammatory response in BMDCs + MPTP midbrain compared to MPTP control mice
    Figure Legend Snippet: Gene expression in midbrain after treatment with MPTP or BMDCs and MPTP. BMDCs were differentiated for 8 days in 20 ng/ml GM-CSF prior to 3 days of pretreatment in media alone. These BMDCs were transferred i.v. one and two weeks prior to intoxication with four doses of 16 mg/kg MPTP. Two days after intoxication, PBS, MPTP and BMDC + MPTP mice were sacrificed and the brain was removed, hemisected and the midbrain was incubated in RNAlater for 24 h prior to freezing at − 80 °C. RNA was isolated from the midbrain, converted to cDNA PCR arrays of proinflammatory genes were run. a Gene expression was determined relative to the PBS control midbrains; n = 3 for PBS and n = 4 for MPTP and MPTP+BMDCs. Fold change was determined using SA Bioscience software. b Ingenuity Pathway Analysis was used to determine the expression of genes associated with the inflammatory response in BMDCs + MPTP midbrain compared to MPTP control mice

    Techniques Used: Expressing, Mouse Assay, Incubation, Isolation, Polymerase Chain Reaction, Software

    22) Product Images from "Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes"

    Article Title: Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes

    Journal: bioRxiv

    doi: 10.1101/2021.07.20.453169

    Distribution of biochemical properties of identified proteins. A) molecular weight (kDa) B) isoelectric point C) number of predicted transmembrane helices. Bars represent the proportion (%) of identified proteins belonging in each range. E = ethanol; FF = flash-freezing; R = RNAlater; RF = RNAlater and flash-freezing; N = NAP buffer; AN = autoclaved NAP buffer.
    Figure Legend Snippet: Distribution of biochemical properties of identified proteins. A) molecular weight (kDa) B) isoelectric point C) number of predicted transmembrane helices. Bars represent the proportion (%) of identified proteins belonging in each range. E = ethanol; FF = flash-freezing; R = RNAlater; RF = RNAlater and flash-freezing; N = NAP buffer; AN = autoclaved NAP buffer.

    Techniques Used: Molecular Weight

    There were no significant differences in total numbers of PSMs, peptides, proteins, and protein groups between samples co-extracted after 1 week of preservation and only minimal differences existed in samples co-extracted after 4 weeks. FF = Flash-freezing, R = RNAlater, RF = RNAlater + flash freezing, N = NAP buffer, AN = Autoclaved NAP buffer, E = 95% Ethanol. 1 week = preserved for one week and first extraction batch. 4 weeks = preserved for 4 weeks and second extraction batch. Bars represent the arithmetic mean (n = 4 for all except E - 4 weeks where n = 3). Error bars represent standard deviation. Asterisks indicate statistical significance (t-test, p-value
    Figure Legend Snippet: There were no significant differences in total numbers of PSMs, peptides, proteins, and protein groups between samples co-extracted after 1 week of preservation and only minimal differences existed in samples co-extracted after 4 weeks. FF = Flash-freezing, R = RNAlater, RF = RNAlater + flash freezing, N = NAP buffer, AN = Autoclaved NAP buffer, E = 95% Ethanol. 1 week = preserved for one week and first extraction batch. 4 weeks = preserved for 4 weeks and second extraction batch. Bars represent the arithmetic mean (n = 4 for all except E - 4 weeks where n = 3). Error bars represent standard deviation. Asterisks indicate statistical significance (t-test, p-value

    Techniques Used: Preserving, Standard Deviation, T-Test

    23) Product Images from "⿿Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples"

    Article Title: ⿿Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples

    Journal: EuPA Open Proteomics

    doi: 10.1016/j.euprot.2015.10.001

    Comparative cellular compartment Gene Ontology annotation of quantified proteins in the colon biopsies to investigate potential method biases toward specific protein types. Top-bar: all quantifiable proteins in the directly frozen (DF) biopsies; middle-bar: proteins uniquely quantified in the DF and RNAlater preserved biopsies; lower-bar: proteins uniquely quantifiable in the immediate formalin-fixed, paraffin-embedded (iFFPE) biopsies. The annotations have been normalized to 100%, and number of included proteins are given for each preservation method.
    Figure Legend Snippet: Comparative cellular compartment Gene Ontology annotation of quantified proteins in the colon biopsies to investigate potential method biases toward specific protein types. Top-bar: all quantifiable proteins in the directly frozen (DF) biopsies; middle-bar: proteins uniquely quantified in the DF and RNAlater preserved biopsies; lower-bar: proteins uniquely quantifiable in the immediate formalin-fixed, paraffin-embedded (iFFPE) biopsies. The annotations have been normalized to 100%, and number of included proteins are given for each preservation method.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Preserving

    Number of identified proteins in the individual colon biopsies, using the direct freezing (DF), RNAlater, immediate formalin-fixed, paraffin-embedded (iFFPE), and 30 min stored formalin-fixed, paraffin-embedded (sFFPE) preparation protocols. Significant changes detected by two-sample t -tests and represented by p -values. NS: not significant, p
    Figure Legend Snippet: Number of identified proteins in the individual colon biopsies, using the direct freezing (DF), RNAlater, immediate formalin-fixed, paraffin-embedded (iFFPE), and 30 min stored formalin-fixed, paraffin-embedded (sFFPE) preparation protocols. Significant changes detected by two-sample t -tests and represented by p -values. NS: not significant, p

    Techniques Used: Formalin-fixed Paraffin-Embedded

    Number of proteins uniquely quantified in the colon biopsies preserved by (a) direct freezing (DF), RNAlater, or immediate formalin-fixed, paraffin-embedded (iFFPE), and (b) iFFPE or 30 min stored formalin-fixed, paraffin-embedded (sFFPE) preservation protocols.
    Figure Legend Snippet: Number of proteins uniquely quantified in the colon biopsies preserved by (a) direct freezing (DF), RNAlater, or immediate formalin-fixed, paraffin-embedded (iFFPE), and (b) iFFPE or 30 min stored formalin-fixed, paraffin-embedded (sFFPE) preservation protocols.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Preserving

    Representative two-dimensional LC⿿MS heat maps from the analysis of the colon biopsies preserved by (a) direct freezing (DF), (b) RNAlater, or (c) immediate formalin-fixed, paraffin-embedded (iFFPE).
    Figure Legend Snippet: Representative two-dimensional LC⿿MS heat maps from the analysis of the colon biopsies preserved by (a) direct freezing (DF), (b) RNAlater, or (c) immediate formalin-fixed, paraffin-embedded (iFFPE).

    Techniques Used: Formalin-fixed Paraffin-Embedded

    Principle component analysis (PCA) scores plot and loadings plot based on principle component 1 and 2, with all protein abundances in the differently preserved colon biopsies from two participants as input. (a) Scores plot of colon biopsies from participant A (filled symbols) and participant B (hollow symbols) were stabilized by direct frozen (DF) (⿠ and ⿡), RNAlater ( and ), immediate formalin-fixed, paraffin-embedded (iFFPE) ( and ), or 30 min stored formalin-fixed, paraffin-embedded (sFFPE) ( and ) preservation protocol. (b) Loadings plot with all quantifiable proteins. Proteins with ±0.4 were analyzed ( and ) were chosen for further analysis. The gene names of the top three extreme proteins on each axis are given. (For interpretation of the references to color in the text, the reader is referred to the web version of this article.)
    Figure Legend Snippet: Principle component analysis (PCA) scores plot and loadings plot based on principle component 1 and 2, with all protein abundances in the differently preserved colon biopsies from two participants as input. (a) Scores plot of colon biopsies from participant A (filled symbols) and participant B (hollow symbols) were stabilized by direct frozen (DF) (⿠ and ⿡), RNAlater ( and ), immediate formalin-fixed, paraffin-embedded (iFFPE) ( and ), or 30 min stored formalin-fixed, paraffin-embedded (sFFPE) ( and ) preservation protocol. (b) Loadings plot with all quantifiable proteins. Proteins with ±0.4 were analyzed ( and ) were chosen for further analysis. The gene names of the top three extreme proteins on each axis are given. (For interpretation of the references to color in the text, the reader is referred to the web version of this article.)

    Techniques Used: Formalin-fixed Paraffin-Embedded, Preserving

    Scatterplots of the log 2 transformed protein abundances of all quantifiable proteins in the colon biopsies, combined by the mean preservation method wise. The protein abundances are plotted against one another on the x - and y- axes, respectively. Correlations between measured protein abundances using the different methods are represented by Pearson⿿s correlation coefficients ( r ), where r = 1 signifies a perfect correlation. Protein abundances in directly frozen (DF) colon biopsies was compared to (a) RNAlater, (b) immediate formalin-fixed, paraffin-embedded (iFFPE), or (c) 30 min stored formalin-fixed, paraffin-embedded (sFFPE), and (d) iFFPE and sFFPE are compared. In all cases r -values > 0.94 were calculated indicating a good correlation. Lines indicates a four fold protein abundance difference in (a⿿c), and a two fold protein abundance difference in (d).
    Figure Legend Snippet: Scatterplots of the log 2 transformed protein abundances of all quantifiable proteins in the colon biopsies, combined by the mean preservation method wise. The protein abundances are plotted against one another on the x - and y- axes, respectively. Correlations between measured protein abundances using the different methods are represented by Pearson⿿s correlation coefficients ( r ), where r = 1 signifies a perfect correlation. Protein abundances in directly frozen (DF) colon biopsies was compared to (a) RNAlater, (b) immediate formalin-fixed, paraffin-embedded (iFFPE), or (c) 30 min stored formalin-fixed, paraffin-embedded (sFFPE), and (d) iFFPE and sFFPE are compared. In all cases r -values > 0.94 were calculated indicating a good correlation. Lines indicates a four fold protein abundance difference in (a⿿c), and a two fold protein abundance difference in (d).

    Techniques Used: Transformation Assay, Preserving, Formalin-fixed Paraffin-Embedded

    24) Product Images from "Crosstalk between Tumor Cells and Macrophages in Stroma Renders Tumor Cells as the Primary Source of MCP-1/CCL2 in Lewis Lung Carcinoma"

    Article Title: Crosstalk between Tumor Cells and Macrophages in Stroma Renders Tumor Cells as the Primary Source of MCP-1/CCL2 in Lewis Lung Carcinoma

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2015.00332

    The expression of MCP-1 in LLC cells isolated from tumors and the role of proinflammatory mediators . (A) Four hundred thousand LLC cells in 100 μl PBS were injected into the flank of female WT or MCP-1 −/− mice. Two weeks later, mice were euthanized, and tumors were excised and cut into halves. One half was stored in RNAlater for total RNA isolation. The other half was minced and digested with collagenase VI for 3 h at room temperature. After removal of tissue debris, cells were rinsed with RPMI 1640 containing 10% FBS, and then plated in a tissue culture plate. Cells were passed for five generations at 1:5 before use. At this stage, the mutated MCP-1 allele was no longer detectable by PCR in tumor cells harvested from MCP-1 −/− mice, indicating that there was no significant contamination by host cells. The expression of MCP-1 mRNA was examined by Northern blotting. All samples (10 μg per lane) were loaded onto a single gel and RNA was transferred to a single membrane. (B) 4T1, B16, or LLC cells were stimulated by 100 ng/ml of LPS or 10 or 100 ng/ml of mouse recombinant TNFα for 6 h. Total RNA was isolated and the expression of MCP-1 mRNA was examined by Northern blotting.
    Figure Legend Snippet: The expression of MCP-1 in LLC cells isolated from tumors and the role of proinflammatory mediators . (A) Four hundred thousand LLC cells in 100 μl PBS were injected into the flank of female WT or MCP-1 −/− mice. Two weeks later, mice were euthanized, and tumors were excised and cut into halves. One half was stored in RNAlater for total RNA isolation. The other half was minced and digested with collagenase VI for 3 h at room temperature. After removal of tissue debris, cells were rinsed with RPMI 1640 containing 10% FBS, and then plated in a tissue culture plate. Cells were passed for five generations at 1:5 before use. At this stage, the mutated MCP-1 allele was no longer detectable by PCR in tumor cells harvested from MCP-1 −/− mice, indicating that there was no significant contamination by host cells. The expression of MCP-1 mRNA was examined by Northern blotting. All samples (10 μg per lane) were loaded onto a single gel and RNA was transferred to a single membrane. (B) 4T1, B16, or LLC cells were stimulated by 100 ng/ml of LPS or 10 or 100 ng/ml of mouse recombinant TNFα for 6 h. Total RNA was isolated and the expression of MCP-1 mRNA was examined by Northern blotting.

    Techniques Used: Expressing, Isolation, Injection, Mouse Assay, Polymerase Chain Reaction, Northern Blot, Recombinant

    The expression of MCP-1 in 4T1, B16, and LLC tumors growing in WT or MCP-1 −/− mice . (A) Four hundred thousand LLC cells in 100 μl PBS were injected into the flank of female WT or MCP-1 −/− mice and the size of each tumor was measured and the volume was calculated. The results are shown as the mean ± SEM; n = 6. (B) The expression of MCP-1 mRNA was examined by Northern blotting 2 weeks after LLC tumor cell inoculation. (C) Serum MCP-1 concentrations were measured by ELISA 2 weeks after LLC tumor cell inoculation. The results are shown as the mean ± SEM. n = 4 for non-tumor-bearing WT mice and n = 5 for tumor-bearing WT or MCP-1 −/− mice. A summary of two experiments. (D,E) One hundred thousand LLC cells in 100 μl PBS were intravenously injected into WT or MCP-1 −/− mice. Two weeks after injection, blood was collected by heart punctured and serum was obtained. Lungs were excised and stored in RNAlater. Total RNA was extracted by TRIzol from lung tumors or adjacent lung tissues and the expression of MCP-1 mRNA expression was examined by Northern blotting. Serum MCP-1 concentration was measured by ELISA. The results are shown as the mean ± SD. n = 2 for tumor-bearing WT or MCP-1 −/− mice. (F) One hundred thousand 4T1 or B16 cells in 100 μl PBS were injected into the mammary pad or the flank of WT or MCP-1 −/− mice, respectively. Two weeks later, the expression of MCP-1 mRNA by tumors was evaluated by Northern blotting. (G) The expression of MCP-1 mRNA in 4T1 tumors and LLC tumors growing in WT mice was evaluated by Nanostring gene profiling. The results are shown as the mean ± SEM.
    Figure Legend Snippet: The expression of MCP-1 in 4T1, B16, and LLC tumors growing in WT or MCP-1 −/− mice . (A) Four hundred thousand LLC cells in 100 μl PBS were injected into the flank of female WT or MCP-1 −/− mice and the size of each tumor was measured and the volume was calculated. The results are shown as the mean ± SEM; n = 6. (B) The expression of MCP-1 mRNA was examined by Northern blotting 2 weeks after LLC tumor cell inoculation. (C) Serum MCP-1 concentrations were measured by ELISA 2 weeks after LLC tumor cell inoculation. The results are shown as the mean ± SEM. n = 4 for non-tumor-bearing WT mice and n = 5 for tumor-bearing WT or MCP-1 −/− mice. A summary of two experiments. (D,E) One hundred thousand LLC cells in 100 μl PBS were intravenously injected into WT or MCP-1 −/− mice. Two weeks after injection, blood was collected by heart punctured and serum was obtained. Lungs were excised and stored in RNAlater. Total RNA was extracted by TRIzol from lung tumors or adjacent lung tissues and the expression of MCP-1 mRNA expression was examined by Northern blotting. Serum MCP-1 concentration was measured by ELISA. The results are shown as the mean ± SD. n = 2 for tumor-bearing WT or MCP-1 −/− mice. (F) One hundred thousand 4T1 or B16 cells in 100 μl PBS were injected into the mammary pad or the flank of WT or MCP-1 −/− mice, respectively. Two weeks later, the expression of MCP-1 mRNA by tumors was evaluated by Northern blotting. (G) The expression of MCP-1 mRNA in 4T1 tumors and LLC tumors growing in WT mice was evaluated by Nanostring gene profiling. The results are shown as the mean ± SEM.

    Techniques Used: Expressing, Mouse Assay, Injection, Northern Blot, Enzyme-linked Immunosorbent Assay, Concentration Assay

    25) Product Images from "The IL-10 homologue encoded by cyprinid herpesvirus 3 is essential neither for viral replication in vitro nor for virulence in vivo"

    Article Title: The IL-10 homologue encoded by cyprinid herpesvirus 3 is essential neither for viral replication in vitro nor for virulence in vivo

    Journal: Veterinary Research

    doi: 10.1186/1297-9716-44-53

    Viral load in gill and kidney. Common carp ( n = 36 fish per tank), with an average weight of 10.7 g ± 3.2 g (mean ± SD), were inoculated by immersion for 2 h in water containing 100 PFU/mL of the indicated CyHV-3 strains. At different times post-inoculation, six infected fish were randomly selected per tank, euthanized and dissected. Six mock-infected fish were used as negative controls. Gill, kidney and spleen were harvested and stored in RNAlater® at −80 °C. DNA was extracted from gill (panel A ) and kidney (panel B ) and analyzed by real-time TaqMan PCR for quantification of viral genome copies. The results are expressed as the means ± SD of the data observed for the 6 fish analyzed per time point. Spleen were treated for quantification of carp gene expression by RT-qPCR (see Figure 11 ).
    Figure Legend Snippet: Viral load in gill and kidney. Common carp ( n = 36 fish per tank), with an average weight of 10.7 g ± 3.2 g (mean ± SD), were inoculated by immersion for 2 h in water containing 100 PFU/mL of the indicated CyHV-3 strains. At different times post-inoculation, six infected fish were randomly selected per tank, euthanized and dissected. Six mock-infected fish were used as negative controls. Gill, kidney and spleen were harvested and stored in RNAlater® at −80 °C. DNA was extracted from gill (panel A ) and kidney (panel B ) and analyzed by real-time TaqMan PCR for quantification of viral genome copies. The results are expressed as the means ± SD of the data observed for the 6 fish analyzed per time point. Spleen were treated for quantification of carp gene expression by RT-qPCR (see Figure 11 ).

    Techniques Used: Fluorescence In Situ Hybridization, Infection, Polymerase Chain Reaction, Expressing, Quantitative RT-PCR

    26) Product Images from "Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean)"

    Article Title: Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean)

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2018.00796

    Confocal laser scanning microscopy (CLSM) and optical images of the microbial mats associated with the cauliflower-like crust (A,C,F) or columnar stromatolites with friable surfaces (B,D,E,G) . (A) Pleurocapsales (red) coated by filamentous microorganisms (green) located at the surface of the microbial mat associated with M17 fixed with formaldehyde and ethanol and stained with Syto9 ® (green) observed with CLSM. (B) Filamentous Cyanobacteria (red) with persistent sheath (blue) detected by CLSM in the microbial mat associated with M12 fixed with formaldehyde and ethanol and stained with Syto9 ® (the Cyanobacteria detected in M15 had the same morphology as in M12). (C) Microbial mat associated with M17 fixed with RNAlater ® , stained with Syto9 ® and observed with CLSM where micrometric coccoid microorganisms are visible in the empty sheath of Pleurocapsales (white star) and in association with refractive dots (blue, white arrow) which are probably elemental sulfur globules produced by the coccoid microorganisms. (D) Filamentous Cyanobacteria detected in the smooth surface of M10 which arbor shorter trichomes than Cyanobacteria detected on M12 and M15. (F) Microbial mat associated with M17 fixed with RNAlater and observed with optical microscopy in which elemental sulfur grains (black arrow) associated with the purple bacteria located around the Pleurocapsales cells (black star) are visible. (E) Red microbial mat associated with M15 fixed with RNA later and stained with Syto9 ® in which refractive grains (blue, white arrow) in rod shaped bacteria probably corresponding to elemental sulfur globules are visible. (G) Transversal cutting of M10 stained with DAPI (blue) and calcein (green), included in LR white resin and observed with CLSM where aragonite grains stained by calcein (white arrow) trapped by filamentous Cyanobacteria stained with DAPI are visible. (H) Colors associated with the CLSM images.
    Figure Legend Snippet: Confocal laser scanning microscopy (CLSM) and optical images of the microbial mats associated with the cauliflower-like crust (A,C,F) or columnar stromatolites with friable surfaces (B,D,E,G) . (A) Pleurocapsales (red) coated by filamentous microorganisms (green) located at the surface of the microbial mat associated with M17 fixed with formaldehyde and ethanol and stained with Syto9 ® (green) observed with CLSM. (B) Filamentous Cyanobacteria (red) with persistent sheath (blue) detected by CLSM in the microbial mat associated with M12 fixed with formaldehyde and ethanol and stained with Syto9 ® (the Cyanobacteria detected in M15 had the same morphology as in M12). (C) Microbial mat associated with M17 fixed with RNAlater ® , stained with Syto9 ® and observed with CLSM where micrometric coccoid microorganisms are visible in the empty sheath of Pleurocapsales (white star) and in association with refractive dots (blue, white arrow) which are probably elemental sulfur globules produced by the coccoid microorganisms. (D) Filamentous Cyanobacteria detected in the smooth surface of M10 which arbor shorter trichomes than Cyanobacteria detected on M12 and M15. (F) Microbial mat associated with M17 fixed with RNAlater and observed with optical microscopy in which elemental sulfur grains (black arrow) associated with the purple bacteria located around the Pleurocapsales cells (black star) are visible. (E) Red microbial mat associated with M15 fixed with RNA later and stained with Syto9 ® in which refractive grains (blue, white arrow) in rod shaped bacteria probably corresponding to elemental sulfur globules are visible. (G) Transversal cutting of M10 stained with DAPI (blue) and calcein (green), included in LR white resin and observed with CLSM where aragonite grains stained by calcein (white arrow) trapped by filamentous Cyanobacteria stained with DAPI are visible. (H) Colors associated with the CLSM images.

    Techniques Used: Confocal Laser Scanning Microscopy, Staining, Produced, Microscopy

    (A) Confocal laser scanning microscopy image of a transversal cutting of the globular crust of M17 embedded in LR white resin, showing the Pleurocapsales colonies (pink/red) topped with grains stained with calcein (green) and filamentous Alphaproteobacteria also strongly stained with calcein (green, white star). (B) Raman mapping superimposed on the CLSM image showing the distribution of the aragonite grains around the Pleurocapsales colonies. (C) Colors associated with the CLSM and Raman mappings. (D) CLSM image of the microbial mat fixed in RNAlater and stained with Syto9 (green) showing the distribution of the Pleurocapsales colonies topped with coccoid microorganisms associated with aragonite grains and filamentous cells on the top. (E) SEM image (at 15 KV, AsB detector) on the same transversal cutting shown in (A,B) , showing aragonite grains associated with the coccoid and filamentous microorganisms associated with the Pleurocapsales. Red stars correspond to aragonite and the green star to hydromagnesite in all images.
    Figure Legend Snippet: (A) Confocal laser scanning microscopy image of a transversal cutting of the globular crust of M17 embedded in LR white resin, showing the Pleurocapsales colonies (pink/red) topped with grains stained with calcein (green) and filamentous Alphaproteobacteria also strongly stained with calcein (green, white star). (B) Raman mapping superimposed on the CLSM image showing the distribution of the aragonite grains around the Pleurocapsales colonies. (C) Colors associated with the CLSM and Raman mappings. (D) CLSM image of the microbial mat fixed in RNAlater and stained with Syto9 (green) showing the distribution of the Pleurocapsales colonies topped with coccoid microorganisms associated with aragonite grains and filamentous cells on the top. (E) SEM image (at 15 KV, AsB detector) on the same transversal cutting shown in (A,B) , showing aragonite grains associated with the coccoid and filamentous microorganisms associated with the Pleurocapsales. Red stars correspond to aragonite and the green star to hydromagnesite in all images.

    Techniques Used: Confocal Laser Scanning Microscopy, Staining

    27) Product Images from "The tick endosymbiont Candidatus Midichloria mitochondrii and selenoproteins are essential for the growth of Rickettsia parkeri in the Gulf Coast tick vector"

    Article Title: The tick endosymbiont Candidatus Midichloria mitochondrii and selenoproteins are essential for the growth of Rickettsia parkeri in the Gulf Coast tick vector

    Journal: Microbiome

    doi: 10.1186/s40168-018-0524-2

    Transovarial and transstadial maintenance of R. parkeri loads during the life stages of A. maculatum ticks. a Estimated R. parkeri load in immature and mature developmental stages of the tick, including the eggs, larva (unfed and blood-fed), nymphs (unfed and blood-fed), and adult males and females (unfed and partially blood-fed). b Time-dependent and tissue-specific R. parkeri load estimated in tick midgut and salivary gland tissues across different time points during tick infestation on sheep. The R. parkeri -infected ticks were infested on sheep and 5–7 ticks were removed from the host on days 2, 4, 5, and 7 post-infestation. Within 2 h of removal from the host, the individual ticks were dissected and their midgut tissues and salivary glands removed. The tissues from individual ticks were stored in RNAlater, RNA was extracted, and qRT-PCR was performed using rompB -specific primers. GAPDH primers were used to estimate the number of R. parkeri copies per tick GAPDH . At least three biological replicates were used in these experiments
    Figure Legend Snippet: Transovarial and transstadial maintenance of R. parkeri loads during the life stages of A. maculatum ticks. a Estimated R. parkeri load in immature and mature developmental stages of the tick, including the eggs, larva (unfed and blood-fed), nymphs (unfed and blood-fed), and adult males and females (unfed and partially blood-fed). b Time-dependent and tissue-specific R. parkeri load estimated in tick midgut and salivary gland tissues across different time points during tick infestation on sheep. The R. parkeri -infected ticks were infested on sheep and 5–7 ticks were removed from the host on days 2, 4, 5, and 7 post-infestation. Within 2 h of removal from the host, the individual ticks were dissected and their midgut tissues and salivary glands removed. The tissues from individual ticks were stored in RNAlater, RNA was extracted, and qRT-PCR was performed using rompB -specific primers. GAPDH primers were used to estimate the number of R. parkeri copies per tick GAPDH . At least three biological replicates were used in these experiments

    Techniques Used: Infection, Quantitative RT-PCR

    Total bacterial load, Francisella- like endosymbiont (FLE) load, and Candidatus Midichloria mitochondrii (CMM) load in tick tissues (midguts, salivary glands, ovaries) from R. parkeri- infected (Rp + ) and uninfected (Rp − ) A. maculatum female ticks. The ticks from both Rp + and Rp − colonies were infested on two separate sheep for blood feeding and 5–15 ticks were removed from the host on day 5 post-infestation. Within 2 h of tick removal from the hosts, the ticks were dissected to isolate their tissues (midgut, salivary glands, and ovarian tissues) and each midgut or salivary gland was individually placed in separate vials and five tick ovaries were pooled in a vial and stored in RNAlater before RNA extraction and cDNA synthesis. Total bacterial loads and FLE and CMM copies/ tick were estimated by qPCR with reference to GAPDH in the tick midgut tissues ( a , b , c ), salivary gland tissues ( d , e , f ) and ovaries ( g , h , i ) in the Rp + ticks (black bars) and the Rp − ticks (gray bars). Rp, R. parkeri ; OV, ovarian tissues; Mg, midguts; Sg, salivary glands
    Figure Legend Snippet: Total bacterial load, Francisella- like endosymbiont (FLE) load, and Candidatus Midichloria mitochondrii (CMM) load in tick tissues (midguts, salivary glands, ovaries) from R. parkeri- infected (Rp + ) and uninfected (Rp − ) A. maculatum female ticks. The ticks from both Rp + and Rp − colonies were infested on two separate sheep for blood feeding and 5–15 ticks were removed from the host on day 5 post-infestation. Within 2 h of tick removal from the hosts, the ticks were dissected to isolate their tissues (midgut, salivary glands, and ovarian tissues) and each midgut or salivary gland was individually placed in separate vials and five tick ovaries were pooled in a vial and stored in RNAlater before RNA extraction and cDNA synthesis. Total bacterial loads and FLE and CMM copies/ tick were estimated by qPCR with reference to GAPDH in the tick midgut tissues ( a , b , c ), salivary gland tissues ( d , e , f ) and ovaries ( g , h , i ) in the Rp + ticks (black bars) and the Rp − ticks (gray bars). Rp, R. parkeri ; OV, ovarian tissues; Mg, midguts; Sg, salivary glands

    Techniques Used: Infection, RNA Extraction, Real-time Polymerase Chain Reaction

    Total bacterial load (BL), Francisella -like endosymbiont (FLE) load, and Candidatus Midichloria mitochondrii (CMM) load in eggs, unfed larva, blood-fed larva, unfed nymphs, and blood-fed nymphs. R. parkeri -infected (Rp + ) and uninfected (Rp − ) A. maculatum gravid females were allowed to oviposit, and approximately 25 days after egg incubation, about 20 mg of the egg masses were sampled from three gravid females separately. When the remaining eggs hatched into larvae, the unfed larvae were allowed to feed on the blood of an individual hamster until repletion occurred. The dropped-off larvae were collected and three from each Rp + and Rp − group were stored in RNAlater. The remaining engorged larvae were incubated for 30 days at which point they molted into nymphal ticks, and the unfed nymphs were blood-fed until repletion. Three engorged nymphs from the Rp + and Rp − groups were stored in RNAlater. Three biological replicates were used for all the treatments. The total bacterial load, FLE, and CMM copies/ tick GAPDH in Rp + and Rp − : Table S1). Total bacterial load, FLE and CMM loads in eggs ( a , b , c ), larva ( d , e , f ), and nymphal ticks ( g , h , i ) are shown. uFL, unfed larva; FL, fed larva; uFN, unfed nymph; FN, fed nymphs
    Figure Legend Snippet: Total bacterial load (BL), Francisella -like endosymbiont (FLE) load, and Candidatus Midichloria mitochondrii (CMM) load in eggs, unfed larva, blood-fed larva, unfed nymphs, and blood-fed nymphs. R. parkeri -infected (Rp + ) and uninfected (Rp − ) A. maculatum gravid females were allowed to oviposit, and approximately 25 days after egg incubation, about 20 mg of the egg masses were sampled from three gravid females separately. When the remaining eggs hatched into larvae, the unfed larvae were allowed to feed on the blood of an individual hamster until repletion occurred. The dropped-off larvae were collected and three from each Rp + and Rp − group were stored in RNAlater. The remaining engorged larvae were incubated for 30 days at which point they molted into nymphal ticks, and the unfed nymphs were blood-fed until repletion. Three engorged nymphs from the Rp + and Rp − groups were stored in RNAlater. Three biological replicates were used for all the treatments. The total bacterial load, FLE, and CMM copies/ tick GAPDH in Rp + and Rp − : Table S1). Total bacterial load, FLE and CMM loads in eggs ( a , b , c ), larva ( d , e , f ), and nymphal ticks ( g , h , i ) are shown. uFL, unfed larva; FL, fed larva; uFN, unfed nymph; FN, fed nymphs

    Techniques Used: Infection, Incubation

    28) Product Images from "Single-cell transcriptomics of malaria parasites"

    Article Title: Single-cell transcriptomics of malaria parasites

    Journal: bioRxiv

    doi: 10.1101/105015

    Dual sorting of two parasite species shows minimal contaminating RNA. (a) Purified asexual late blood stage of GFP P. falciparum and mCherry P. berghei were mixed at a 1:1 ratio, inactivated in RNALater, and sorted individually by flow cytometry, gated on respective fluorescent channels. The proportion of shared contaminating transcripts between pairs of cells was low for P. falciparum transcripts in P. berghei cells (b) and even lower for P. berghei transcripts in P. falciparum cells (c). Overall there were 273 unique P. falciparum transcripts contaminating the P. berghei transcriptomes, although no cell had more than 37 contaminating transcripts and no pair of cells shared more than 17. There was a total of 258 P. berghei transcripts contaminating P. falciparum transcriptomes, although no cell had more than 32 of these and no pair of cells shared more than 10. The data suggest that P. falciparum schizonts cause more contamination than P. berghei schizonts. More commonly occurring, contaminating transcripts are more highly expressed in their cells of origin for both P. falciparum transcripts contaminating P. berghei cells (d) and P. berghei transcripts contaminating P. falciparum cells (e). This suggests that contaminants reflect the observed pool of transcripts.
    Figure Legend Snippet: Dual sorting of two parasite species shows minimal contaminating RNA. (a) Purified asexual late blood stage of GFP P. falciparum and mCherry P. berghei were mixed at a 1:1 ratio, inactivated in RNALater, and sorted individually by flow cytometry, gated on respective fluorescent channels. The proportion of shared contaminating transcripts between pairs of cells was low for P. falciparum transcripts in P. berghei cells (b) and even lower for P. berghei transcripts in P. falciparum cells (c). Overall there were 273 unique P. falciparum transcripts contaminating the P. berghei transcriptomes, although no cell had more than 37 contaminating transcripts and no pair of cells shared more than 17. There was a total of 258 P. berghei transcripts contaminating P. falciparum transcriptomes, although no cell had more than 32 of these and no pair of cells shared more than 10. The data suggest that P. falciparum schizonts cause more contamination than P. berghei schizonts. More commonly occurring, contaminating transcripts are more highly expressed in their cells of origin for both P. falciparum transcripts contaminating P. berghei cells (d) and P. berghei transcripts contaminating P. falciparum cells (e). This suggests that contaminants reflect the observed pool of transcripts.

    Techniques Used: Purification, Flow Cytometry

    29) Product Images from "Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes"

    Article Title: Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes

    Journal: bioRxiv

    doi: 10.1101/2021.07.20.453169

    Distribution of biochemical properties of identified proteins. A) molecular weight (kDa) B) isoelectric point C) number of predicted transmembrane helices. Bars represent the proportion (%) of identified proteins belonging in each range. E = ethanol; FF = flash-freezing; R = RNAlater; RF = RNAlater and flash-freezing; N = NAP buffer; AN = autoclaved NAP buffer.
    Figure Legend Snippet: Distribution of biochemical properties of identified proteins. A) molecular weight (kDa) B) isoelectric point C) number of predicted transmembrane helices. Bars represent the proportion (%) of identified proteins belonging in each range. E = ethanol; FF = flash-freezing; R = RNAlater; RF = RNAlater and flash-freezing; N = NAP buffer; AN = autoclaved NAP buffer.

    Techniques Used: Molecular Weight

    There were no significant differences in total numbers of PSMs, peptides, proteins, and protein groups between samples co-extracted after 1 week of preservation and only minimal differences existed in samples co-extracted after 4 weeks. FF = Flash-freezing, R = RNAlater, RF = RNAlater + flash freezing, N = NAP buffer, AN = Autoclaved NAP buffer, E = 95% Ethanol. 1 week = preserved for one week and first extraction batch. 4 weeks = preserved for 4 weeks and second extraction batch. Bars represent the arithmetic mean (n = 4 for all except E - 4 weeks where n = 3). Error bars represent standard deviation. Asterisks indicate statistical significance (t-test, p-value
    Figure Legend Snippet: There were no significant differences in total numbers of PSMs, peptides, proteins, and protein groups between samples co-extracted after 1 week of preservation and only minimal differences existed in samples co-extracted after 4 weeks. FF = Flash-freezing, R = RNAlater, RF = RNAlater + flash freezing, N = NAP buffer, AN = Autoclaved NAP buffer, E = 95% Ethanol. 1 week = preserved for one week and first extraction batch. 4 weeks = preserved for 4 weeks and second extraction batch. Bars represent the arithmetic mean (n = 4 for all except E - 4 weeks where n = 3). Error bars represent standard deviation. Asterisks indicate statistical significance (t-test, p-value

    Techniques Used: Preserving, Standard Deviation, T-Test

    30) Product Images from "A toolkit for studying Varroa genomics and transcriptomics: preservation, extraction, and sequencing library preparation"

    Article Title: A toolkit for studying Varroa genomics and transcriptomics: preservation, extraction, and sequencing library preparation

    Journal: BMC Genomics

    doi: 10.1186/s12864-020-07363-7

    Representative bioanalyzer result of Varroa mite total RNA, extracted 21 days post-treatment. Control samples that were snap-frozen and stored at -80 °C show minimal noise and a clean 18S peak, while ethanol samples at room temperature and 4 °C also showed a similar 18S peak; however, with more degradation products. Mites stored in RNAlater and TRIzol had degraded and did not show a peak at 18S, indicating that RNA preservation was not successful. This suggests that weeks of storage in ethanol, even at room temperature, have little effect on RNA integrity
    Figure Legend Snippet: Representative bioanalyzer result of Varroa mite total RNA, extracted 21 days post-treatment. Control samples that were snap-frozen and stored at -80 °C show minimal noise and a clean 18S peak, while ethanol samples at room temperature and 4 °C also showed a similar 18S peak; however, with more degradation products. Mites stored in RNAlater and TRIzol had degraded and did not show a peak at 18S, indicating that RNA preservation was not successful. This suggests that weeks of storage in ethanol, even at room temperature, have little effect on RNA integrity

    Techniques Used: Preserving

    31) Product Images from "The effect of spaceflight on the gravity-sensing auxin gradient of roots: GFP reporter gene microscopy on orbit"

    Article Title: The effect of spaceflight on the gravity-sensing auxin gradient of roots: GFP reporter gene microscopy on orbit

    Journal: NPJ Microgravity

    doi: 10.1038/npjmgrav.2015.23

    Distribution of pDR5r::GFP expression for spaceflight and ground control samples from the APEX03-2 and CARA experiments. In each case, the merged image and age of plant is shown on left and the GFP signal is shown on the right. Images ( a – h ) were collected live with the LMM on the ISS and with the LMM Ground Interface Unit (GIU) at Glenn Research Center. ( a ) APEX 4d ground control; ( b ) APEX 4d spaceflight; ( c ) APEX 8d ground control; ( d ) APEX 8d spaceflight; ( e ) CARA 5d ground control; ( f ) CARA 5d spaceflight; ( g ) CARA 8d ground control; ( h ) CARA 8d spaceflight. Images ( i and j ) show the distribution of DR5r::GFP (green) in RNAlater-preserved APEX03-2 Arabidopsis roots counterstained with Calcofluor White to outline cell walls (blue) and imaged with a Leica TSC-SP5 confocal microscope. In both cases, a single rotational view of a 3D projection of multiple Z-sections is presented in the right-hand panel. ( i ) APEX 4d ground control; ( j ) APEX 4d spaceflight. The complete animated 3D projections for ( i ) and ( j ) can be found in Supplementary Movie S1 ( i ) and Supplementary Movie S2 ( j ). d, days; GFP, green fluorescent protein; ISS, Internationa Space Station; 3D, three-dimensional.
    Figure Legend Snippet: Distribution of pDR5r::GFP expression for spaceflight and ground control samples from the APEX03-2 and CARA experiments. In each case, the merged image and age of plant is shown on left and the GFP signal is shown on the right. Images ( a – h ) were collected live with the LMM on the ISS and with the LMM Ground Interface Unit (GIU) at Glenn Research Center. ( a ) APEX 4d ground control; ( b ) APEX 4d spaceflight; ( c ) APEX 8d ground control; ( d ) APEX 8d spaceflight; ( e ) CARA 5d ground control; ( f ) CARA 5d spaceflight; ( g ) CARA 8d ground control; ( h ) CARA 8d spaceflight. Images ( i and j ) show the distribution of DR5r::GFP (green) in RNAlater-preserved APEX03-2 Arabidopsis roots counterstained with Calcofluor White to outline cell walls (blue) and imaged with a Leica TSC-SP5 confocal microscope. In both cases, a single rotational view of a 3D projection of multiple Z-sections is presented in the right-hand panel. ( i ) APEX 4d ground control; ( j ) APEX 4d spaceflight. The complete animated 3D projections for ( i ) and ( j ) can be found in Supplementary Movie S1 ( i ) and Supplementary Movie S2 ( j ). d, days; GFP, green fluorescent protein; ISS, Internationa Space Station; 3D, three-dimensional.

    Techniques Used: Expressing, Microscopy

    Distribution of other auxin and cytokinin-sensitive GFP reporters. In each case, the merged image and age of plant in shown on left and the GFP signal is shown on the right. Images ( a – d ) were collected from RNAlater-preserved APEX03-2 4d samples returned to Earth, with a Leica TSC-SP5 confocal microscope. Images ( e – l ) collected live with the Light Microscopy Module (LMM) on the ISS and with the LMM Ground Interface Unit (GIU) at Glenn Research Center. ( a ) APEX 4d ground control, pTAA1::TAA1–GFP; ( b ) APEX 4d spaceflight, pTAA1::TAA1–GFP; ( c ) APEX 4d ground control, pSCR::SCR–GFP; ( d ) APEX 4d spaceflight, pSCR::SCR–GFP; ( e ) APEX 4d ground control, pTAA1::TAA1–GFP; ( f ) APEX 4d spaceflight, pTAA1::TAA1–GFP; ( g ) APEX 8d ground control, pSCR::SCR–GFP; ( h ) APEX 8d spaceflight, pSCR::SCR–GFP; ( i ) CARA 5d ground control, pARR5::GFP; ( j ) CARA 5d spaceflight, pARR5::GFP; ( k ) CARA 8d ground control, pARR5::GFP; ( l ) CARA 8d spaceflight, pARR5::GFP. In addition, animated 3D projections for ( a ) and can be found in Supplementary Movie S3 , and ( b ) in Supplementary Movie S4 . d, days; GFP, green fluorescent protein.
    Figure Legend Snippet: Distribution of other auxin and cytokinin-sensitive GFP reporters. In each case, the merged image and age of plant in shown on left and the GFP signal is shown on the right. Images ( a – d ) were collected from RNAlater-preserved APEX03-2 4d samples returned to Earth, with a Leica TSC-SP5 confocal microscope. Images ( e – l ) collected live with the Light Microscopy Module (LMM) on the ISS and with the LMM Ground Interface Unit (GIU) at Glenn Research Center. ( a ) APEX 4d ground control, pTAA1::TAA1–GFP; ( b ) APEX 4d spaceflight, pTAA1::TAA1–GFP; ( c ) APEX 4d ground control, pSCR::SCR–GFP; ( d ) APEX 4d spaceflight, pSCR::SCR–GFP; ( e ) APEX 4d ground control, pTAA1::TAA1–GFP; ( f ) APEX 4d spaceflight, pTAA1::TAA1–GFP; ( g ) APEX 8d ground control, pSCR::SCR–GFP; ( h ) APEX 8d spaceflight, pSCR::SCR–GFP; ( i ) CARA 5d ground control, pARR5::GFP; ( j ) CARA 5d spaceflight, pARR5::GFP; ( k ) CARA 8d ground control, pARR5::GFP; ( l ) CARA 8d spaceflight, pARR5::GFP. In addition, animated 3D projections for ( a ) and can be found in Supplementary Movie S3 , and ( b ) in Supplementary Movie S4 . d, days; GFP, green fluorescent protein.

    Techniques Used: Microscopy, Light Microscopy

    32) Product Images from "Traumatic brain injury induces long-lasting changes in immune and regenerative signaling"

    Article Title: Traumatic brain injury induces long-lasting changes in immune and regenerative signaling

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0214741

    Schematic of experimental design. Rats were subjected to fluid percussion injury (FPI) and survived for 24 hours, 2 weeks, 3 month, 6 month, and 12 months. At the time of sacrifice, whole hippocampal and cortex tissue (beneath the injury site) were manually dissected and stored in RNALater at 4° C until processed for genomic analysis. (* 1 and 2 month time points were subsequently added to the experimental design after the initial analysis was completed for animals survived up to 1 year post-FPI).
    Figure Legend Snippet: Schematic of experimental design. Rats were subjected to fluid percussion injury (FPI) and survived for 24 hours, 2 weeks, 3 month, 6 month, and 12 months. At the time of sacrifice, whole hippocampal and cortex tissue (beneath the injury site) were manually dissected and stored in RNALater at 4° C until processed for genomic analysis. (* 1 and 2 month time points were subsequently added to the experimental design after the initial analysis was completed for animals survived up to 1 year post-FPI).

    Techniques Used:

    33) Product Images from "Age specific responses to acute inhalation of diffusion flame soot particles: Cellular injury and the airway antioxidant response"

    Article Title: Age specific responses to acute inhalation of diffusion flame soot particles: Cellular injury and the airway antioxidant response

    Journal: Inhalation toxicology

    doi: 10.3109/08958378.2010.513403

    Heatmaps of all genes that were differentially expressed in the airways of rats as a combination of age or exposure. RNA was isolated from microdissected intrapulmonary airways obtained from RNAlater stabilized lung tissue and quantified using the RT
    Figure Legend Snippet: Heatmaps of all genes that were differentially expressed in the airways of rats as a combination of age or exposure. RNA was isolated from microdissected intrapulmonary airways obtained from RNAlater stabilized lung tissue and quantified using the RT

    Techniques Used: Isolation

    34) Product Images from "Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana"

    Article Title: Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

    Journal: BMC Genomics

    doi: 10.1186/s12864-019-5554-z

    The phenotype of Arabidopsis seedlings grown on the ISS and on the ground. a A view of the APEX03–2 experiment growing inside Veggie on the ISS (left) and a view of plates installed in the ground Veggie unit to illustrate the configuration of plates installed vertically in racks. b Arabidopsis thaliana (WS) seedlings were grown under constant LED light conditions in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS for 11 days. Corresponding ground control plants were grown in the Veggie hardware within the ISS Environmental Simulation (ISSES) chamber at Kennedy Space Center for 11 days. Each plate was considered a biological replicate and a total of 6 plates were used in this experiment. All three biological replicates for both spaceflight and ground control are represented. c The workflow of transcriptome and DNA methylome analysis. Plant materials harvested in RNAlater were dissected into root and leaf tissues. Total RNA DNA were isolated separately, and the differential analyses were conducted in an organ-specific manner comparing the effects of spaceflight (FT) vs ground control (GC) in the roots and leaves
    Figure Legend Snippet: The phenotype of Arabidopsis seedlings grown on the ISS and on the ground. a A view of the APEX03–2 experiment growing inside Veggie on the ISS (left) and a view of plates installed in the ground Veggie unit to illustrate the configuration of plates installed vertically in racks. b Arabidopsis thaliana (WS) seedlings were grown under constant LED light conditions in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS for 11 days. Corresponding ground control plants were grown in the Veggie hardware within the ISS Environmental Simulation (ISSES) chamber at Kennedy Space Center for 11 days. Each plate was considered a biological replicate and a total of 6 plates were used in this experiment. All three biological replicates for both spaceflight and ground control are represented. c The workflow of transcriptome and DNA methylome analysis. Plant materials harvested in RNAlater were dissected into root and leaf tissues. Total RNA DNA were isolated separately, and the differential analyses were conducted in an organ-specific manner comparing the effects of spaceflight (FT) vs ground control (GC) in the roots and leaves

    Techniques Used: Isolation

    35) Product Images from "A toolkit for studying Varroa genomics and transcriptomics: Preservation, extraction, and sequencing library preparation"

    Article Title: A toolkit for studying Varroa genomics and transcriptomics: Preservation, extraction, and sequencing library preparation

    Journal: bioRxiv

    doi: 10.1101/2020.08.17.255083

    Representative bioanalyzer result of Varroa mite total RNA, extracted 21 days post-treatment. Control samples that were snap-frozen and stored at −80°C show minimal noise and a clean 18S peak, while ethanol samples at room temperature and 4°C also showed a similar 18S peak; however, with more degradation products. Mites stored in RNAlater and TRIzol had degraded and did not show a peak at 18S, indicating that RNA preservation was not successful. This suggests that weeks of storage in ethanol, even at room temperature, have little effect on RNA integrity.
    Figure Legend Snippet: Representative bioanalyzer result of Varroa mite total RNA, extracted 21 days post-treatment. Control samples that were snap-frozen and stored at −80°C show minimal noise and a clean 18S peak, while ethanol samples at room temperature and 4°C also showed a similar 18S peak; however, with more degradation products. Mites stored in RNAlater and TRIzol had degraded and did not show a peak at 18S, indicating that RNA preservation was not successful. This suggests that weeks of storage in ethanol, even at room temperature, have little effect on RNA integrity.

    Techniques Used: Preserving

    36) Product Images from "Optimization of sperm RNA processing for developmental research"

    Article Title: Optimization of sperm RNA processing for developmental research

    Journal: Scientific Reports

    doi: 10.1038/s41598-020-68486-1

    Effect of total sperm RNA processing method on RT-qPCR. ( A ) Melting curve of− 80 °C storage, snap-frozen, without DNase RNA isolation as a representative of normal RT-qPCR data from good quality RNA (260/280 ratio > 1.7) and− 80 °C storage, RNAlater-treated, with DNase RNA isolation as a representative of unnormal RT-qPCR data from bad quality RNA (260/280 ratio
    Figure Legend Snippet: Effect of total sperm RNA processing method on RT-qPCR. ( A ) Melting curve of− 80 °C storage, snap-frozen, without DNase RNA isolation as a representative of normal RT-qPCR data from good quality RNA (260/280 ratio > 1.7) and− 80 °C storage, RNAlater-treated, with DNase RNA isolation as a representative of unnormal RT-qPCR data from bad quality RNA (260/280 ratio

    Techniques Used: Quantitative RT-PCR, Isolation

    37) Product Images from "The tick endosymbiont Candidatus Midichloria mitochondrii and selenoproteins are essential for the growth of Rickettsia parkeri in the Gulf Coast tick vector"

    Article Title: The tick endosymbiont Candidatus Midichloria mitochondrii and selenoproteins are essential for the growth of Rickettsia parkeri in the Gulf Coast tick vector

    Journal: Microbiome

    doi: 10.1186/s40168-018-0524-2

    Transovarial and transstadial maintenance of R. parkeri loads during the life stages of A. maculatum ticks. a Estimated R. parkeri load in immature and mature developmental stages of the tick, including the eggs, larva (unfed and blood-fed), nymphs (unfed and blood-fed), and adult males and females (unfed and partially blood-fed). b Time-dependent and tissue-specific R. parkeri load estimated in tick midgut and salivary gland tissues across different time points during tick infestation on sheep. The R. parkeri -infected ticks were infested on sheep and 5–7 ticks were removed from the host on days 2, 4, 5, and 7 post-infestation. Within 2 h of removal from the host, the individual ticks were dissected and their midgut tissues and salivary glands removed. The tissues from individual ticks were stored in RNAlater, RNA was extracted, and qRT-PCR was performed using rompB -specific primers. GAPDH primers were used to estimate the number of R. parkeri copies per tick GAPDH . At least three biological replicates were used in these experiments
    Figure Legend Snippet: Transovarial and transstadial maintenance of R. parkeri loads during the life stages of A. maculatum ticks. a Estimated R. parkeri load in immature and mature developmental stages of the tick, including the eggs, larva (unfed and blood-fed), nymphs (unfed and blood-fed), and adult males and females (unfed and partially blood-fed). b Time-dependent and tissue-specific R. parkeri load estimated in tick midgut and salivary gland tissues across different time points during tick infestation on sheep. The R. parkeri -infected ticks were infested on sheep and 5–7 ticks were removed from the host on days 2, 4, 5, and 7 post-infestation. Within 2 h of removal from the host, the individual ticks were dissected and their midgut tissues and salivary glands removed. The tissues from individual ticks were stored in RNAlater, RNA was extracted, and qRT-PCR was performed using rompB -specific primers. GAPDH primers were used to estimate the number of R. parkeri copies per tick GAPDH . At least three biological replicates were used in these experiments

    Techniques Used: Infection, Quantitative RT-PCR

    Total bacterial load, Francisella- like endosymbiont (FLE) load, and Candidatus Midichloria mitochondrii (CMM) load in tick tissues (midguts, salivary glands, ovaries) from R. parkeri- infected (Rp + ) and uninfected (Rp − ) A. maculatum female ticks. The ticks from both Rp + and Rp − colonies were infested on two separate sheep for blood feeding and 5–15 ticks were removed from the host on day 5 post-infestation. Within 2 h of tick removal from the hosts, the ticks were dissected to isolate their tissues (midgut, salivary glands, and ovarian tissues) and each midgut or salivary gland was individually placed in separate vials and five tick ovaries were pooled in a vial and stored in RNAlater before RNA extraction and cDNA synthesis. Total bacterial loads and FLE and CMM copies/ tick were estimated by qPCR with reference to GAPDH in the tick midgut tissues ( a , b , c ), salivary gland tissues ( d , e , f ) and ovaries ( g , h , i ) in the Rp + ticks (black bars) and the Rp − ticks (gray bars). Rp, R. parkeri ; OV, ovarian tissues; Mg, midguts; Sg, salivary glands
    Figure Legend Snippet: Total bacterial load, Francisella- like endosymbiont (FLE) load, and Candidatus Midichloria mitochondrii (CMM) load in tick tissues (midguts, salivary glands, ovaries) from R. parkeri- infected (Rp + ) and uninfected (Rp − ) A. maculatum female ticks. The ticks from both Rp + and Rp − colonies were infested on two separate sheep for blood feeding and 5–15 ticks were removed from the host on day 5 post-infestation. Within 2 h of tick removal from the hosts, the ticks were dissected to isolate their tissues (midgut, salivary glands, and ovarian tissues) and each midgut or salivary gland was individually placed in separate vials and five tick ovaries were pooled in a vial and stored in RNAlater before RNA extraction and cDNA synthesis. Total bacterial loads and FLE and CMM copies/ tick were estimated by qPCR with reference to GAPDH in the tick midgut tissues ( a , b , c ), salivary gland tissues ( d , e , f ) and ovaries ( g , h , i ) in the Rp + ticks (black bars) and the Rp − ticks (gray bars). Rp, R. parkeri ; OV, ovarian tissues; Mg, midguts; Sg, salivary glands

    Techniques Used: Infection, RNA Extraction, Real-time Polymerase Chain Reaction

    Total bacterial load (BL), Francisella -like endosymbiont (FLE) load, and Candidatus Midichloria mitochondrii (CMM) load in eggs, unfed larva, blood-fed larva, unfed nymphs, and blood-fed nymphs. R. parkeri -infected (Rp + ) and uninfected (Rp − ) A. maculatum gravid females were allowed to oviposit, and approximately 25 days after egg incubation, about 20 mg of the egg masses were sampled from three gravid females separately. When the remaining eggs hatched into larvae, the unfed larvae were allowed to feed on the blood of an individual hamster until repletion occurred. The dropped-off larvae were collected and three from each Rp + and Rp − group were stored in RNAlater. The remaining engorged larvae were incubated for 30 days at which point they molted into nymphal ticks, and the unfed nymphs were blood-fed until repletion. Three engorged nymphs from the Rp + and Rp − groups were stored in RNAlater. Three biological replicates were used for all the treatments. The total bacterial load, FLE, and CMM copies/ tick GAPDH in Rp + and Rp − ticks were determined using gene-specific primers (Additional file 5 : Table S1). Total bacterial load, FLE and CMM loads in eggs ( a , b , c ), larva ( d , e , f ), and nymphal ticks ( g , h , i ) are shown. uFL, unfed larva; FL, fed larva; uFN, unfed nymph; FN, fed nymphs
    Figure Legend Snippet: Total bacterial load (BL), Francisella -like endosymbiont (FLE) load, and Candidatus Midichloria mitochondrii (CMM) load in eggs, unfed larva, blood-fed larva, unfed nymphs, and blood-fed nymphs. R. parkeri -infected (Rp + ) and uninfected (Rp − ) A. maculatum gravid females were allowed to oviposit, and approximately 25 days after egg incubation, about 20 mg of the egg masses were sampled from three gravid females separately. When the remaining eggs hatched into larvae, the unfed larvae were allowed to feed on the blood of an individual hamster until repletion occurred. The dropped-off larvae were collected and three from each Rp + and Rp − group were stored in RNAlater. The remaining engorged larvae were incubated for 30 days at which point they molted into nymphal ticks, and the unfed nymphs were blood-fed until repletion. Three engorged nymphs from the Rp + and Rp − groups were stored in RNAlater. Three biological replicates were used for all the treatments. The total bacterial load, FLE, and CMM copies/ tick GAPDH in Rp + and Rp − ticks were determined using gene-specific primers (Additional file 5 : Table S1). Total bacterial load, FLE and CMM loads in eggs ( a , b , c ), larva ( d , e , f ), and nymphal ticks ( g , h , i ) are shown. uFL, unfed larva; FL, fed larva; uFN, unfed nymph; FN, fed nymphs

    Techniques Used: Infection, Incubation

    38) Product Images from "The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia"

    Article Title: The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0175066

    Proportion of sequences belonging to each phylum (abundance data) retrieved from three ARMS using four processing methods (SWET, KEW, MILL, and NOAA) and four storage techniques: 1 month at -20°C in EtOH, DMSO, or RNAlater (RNAL), or samples were immediately extracted (IMM). The category “Other animals” represents Hemichordata, Entoprocta, Rotifera, Tardigrada, Xenacoelomorpha, Gastrotricha, Nemertea, Platyhelminths, Sipuncula and Nematoda.
    Figure Legend Snippet: Proportion of sequences belonging to each phylum (abundance data) retrieved from three ARMS using four processing methods (SWET, KEW, MILL, and NOAA) and four storage techniques: 1 month at -20°C in EtOH, DMSO, or RNAlater (RNAL), or samples were immediately extracted (IMM). The category “Other animals” represents Hemichordata, Entoprocta, Rotifera, Tardigrada, Xenacoelomorpha, Gastrotricha, Nemertea, Platyhelminths, Sipuncula and Nematoda.

    Techniques Used:

    Multidimensional scaling of the sessile eukaryotic community (OTU abundance data; no singletons) retrieved from three ARMS using four processing methods (NOAA, SWET, KEW and MILL) and four storage techniques: 1 month at -20°C in EtOH, DMSO or RNAlater, or samples were immediately extracted (IMM). Clusters represent similarity between samples (50%), based on a Bray-Curtis similarity matrix.
    Figure Legend Snippet: Multidimensional scaling of the sessile eukaryotic community (OTU abundance data; no singletons) retrieved from three ARMS using four processing methods (NOAA, SWET, KEW and MILL) and four storage techniques: 1 month at -20°C in EtOH, DMSO or RNAlater, or samples were immediately extracted (IMM). Clusters represent similarity between samples (50%), based on a Bray-Curtis similarity matrix.

    Techniques Used:

    Group average hierarchical clustering with SIMPROF tests (red bars) of the community found on three ARMS via NGS and CPCe. Community data are based on the percentage of the sessile community belonging to Rhodophyta, Chlorophyta, Porifera, Tunicata, Bryozoa, sessile Mollusca and Anthrozoa. Samples represent different processing methods (NOAA, SWET, MILL and KEW), different storage methods (EtOH, RNAlater, DMSO and Immediate extraction of DNA (IMM)) and image analysis of each overall ARMS (CPCe). Clustering is based on a Bray-Curtis similarity matrix of relative percentages of each group.
    Figure Legend Snippet: Group average hierarchical clustering with SIMPROF tests (red bars) of the community found on three ARMS via NGS and CPCe. Community data are based on the percentage of the sessile community belonging to Rhodophyta, Chlorophyta, Porifera, Tunicata, Bryozoa, sessile Mollusca and Anthrozoa. Samples represent different processing methods (NOAA, SWET, MILL and KEW), different storage methods (EtOH, RNAlater, DMSO and Immediate extraction of DNA (IMM)) and image analysis of each overall ARMS (CPCe). Clustering is based on a Bray-Curtis similarity matrix of relative percentages of each group.

    Techniques Used: Next-Generation Sequencing

    39) Product Images from "Inappropriateness of RNAlater to preserve Caenorhabditis elegans for RNA extraction"

    Article Title: Inappropriateness of RNAlater to preserve Caenorhabditis elegans for RNA extraction

    Journal: MethodsX

    doi: 10.1016/j.mex.2019.10.015

    Effect of worm storage conditions on RNA yield. Four store conditions:(I) fresh worms (no storage); (II) stored in RNAlater (Ambion, Cat.#AM7021) at 4 °C for 24 h followed by storage at −80 °C until test; (III) stored in RNase-free water without RNAlater at 4 °C for 24 h followed by storage at −80 °C until test; (IV) frozen in liquid nitrogen and then stored at −80 °C until test. Results are presented as mean ± S.D. (n = 3). Different letters represent a significant difference ( P ≤ 0.05).
    Figure Legend Snippet: Effect of worm storage conditions on RNA yield. Four store conditions:(I) fresh worms (no storage); (II) stored in RNAlater (Ambion, Cat.#AM7021) at 4 °C for 24 h followed by storage at −80 °C until test; (III) stored in RNase-free water without RNAlater at 4 °C for 24 h followed by storage at −80 °C until test; (IV) frozen in liquid nitrogen and then stored at −80 °C until test. Results are presented as mean ± S.D. (n = 3). Different letters represent a significant difference ( P ≤ 0.05).

    Techniques Used:

    40) Product Images from "Administration of FTY720 during Tourniquet-Induced Limb Ischemia Reperfusion Injury Attenuates Systemic Inflammation"

    Article Title: Administration of FTY720 during Tourniquet-Induced Limb Ischemia Reperfusion Injury Attenuates Systemic Inflammation

    Journal: Mediators of Inflammation

    doi: 10.1155/2017/4594035

    Differential expression of selected genes in ischemic muscle, liver, and lung tissue in FTY720-treated rats (■) versus vehicle control-treated rats (•) following tourniquet-induced hind limb ischemia. Tissues at the indicated time point post-IRI were stored in RNALater and subsequently processed for mRNA. cDNA conversion of 1 μ g of RNA was performed by RT-PCR followed by semiquantitative real-time PCR for gene expression analysis using the 2 −ΔΔCT method. A custom low-density array panel of 88 genes relevant to ischemia-reperfusion injury was selected for the analysis. For each tissue, gene expression was quantified relative to naïve control animals. ∗ P
    Figure Legend Snippet: Differential expression of selected genes in ischemic muscle, liver, and lung tissue in FTY720-treated rats (■) versus vehicle control-treated rats (•) following tourniquet-induced hind limb ischemia. Tissues at the indicated time point post-IRI were stored in RNALater and subsequently processed for mRNA. cDNA conversion of 1 μ g of RNA was performed by RT-PCR followed by semiquantitative real-time PCR for gene expression analysis using the 2 −ΔΔCT method. A custom low-density array panel of 88 genes relevant to ischemia-reperfusion injury was selected for the analysis. For each tissue, gene expression was quantified relative to naïve control animals. ∗ P

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

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    Thermo Fisher rnalater solution
    Lack of immune stimulatory effect of SG220 in vitro and in vivo . ( a ) In vitro analysis. Twenty nmol/l sshRNAs SG220 or SG273 were transfected into human MRC-5 cells in triplicate. Untransfected (N/A) cells and cells transfected with Lipofectamine 2000 alone (Lipo2K) served as negative controls. The numbers shown are the mean and standard deviations of the mean of the indicated cytokine mRNAs relative to the untransfected control and normalized to GAPDH. ( b, c ) In vivo analysis. CD1 ICR mice were administered 2.5 mg/kg LNP-formulated sshRNA (SG220) or LNP-formulated control siRNAs (LUC-U/U, LUC) by intravenous injection. At the designated time point, blood was collected by cardiac puncture and processed as plasma for cytokine determination, and liver was excised and placed in <t>RNAlater</t> (Sigma–Aldrich) for IFIT1 mRNA analysis. The values shown are mean and standard deviation of measurements from each group of four mice. ( b ) Plasma cytokines (left) and liver IFIT mRNA (right), determined 4 hours after administration. ( c ) Time course of SG220-mediated plasma cytokine (left) and liver IFIT1 mRNA (right) induction. LNP, lipid nanoparticles.
    Rnalater Solution, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rnalater
    Distribution of biochemical properties of identified proteins. A) molecular weight (kDa) B) isoelectric point C) number of predicted transmembrane helices. Bars represent the proportion (%) of identified proteins belonging in each range. E = ethanol; FF = flash-freezing; R = <t>RNAlater;</t> RF = RNAlater and flash-freezing; N = NAP buffer; AN = autoclaved NAP buffer.
    Rnalater, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Lack of immune stimulatory effect of SG220 in vitro and in vivo . ( a ) In vitro analysis. Twenty nmol/l sshRNAs SG220 or SG273 were transfected into human MRC-5 cells in triplicate. Untransfected (N/A) cells and cells transfected with Lipofectamine 2000 alone (Lipo2K) served as negative controls. The numbers shown are the mean and standard deviations of the mean of the indicated cytokine mRNAs relative to the untransfected control and normalized to GAPDH. ( b, c ) In vivo analysis. CD1 ICR mice were administered 2.5 mg/kg LNP-formulated sshRNA (SG220) or LNP-formulated control siRNAs (LUC-U/U, LUC) by intravenous injection. At the designated time point, blood was collected by cardiac puncture and processed as plasma for cytokine determination, and liver was excised and placed in RNAlater (Sigma–Aldrich) for IFIT1 mRNA analysis. The values shown are mean and standard deviation of measurements from each group of four mice. ( b ) Plasma cytokines (left) and liver IFIT mRNA (right), determined 4 hours after administration. ( c ) Time course of SG220-mediated plasma cytokine (left) and liver IFIT1 mRNA (right) induction. LNP, lipid nanoparticles.

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: Minimal-length Synthetic shRNAs Formulated with Lipid Nanoparticles are Potent Inhibitors of Hepatitis C Virus IRES-linked Gene Expression in Mice

    doi: 10.1038/mtna.2013.50

    Figure Lengend Snippet: Lack of immune stimulatory effect of SG220 in vitro and in vivo . ( a ) In vitro analysis. Twenty nmol/l sshRNAs SG220 or SG273 were transfected into human MRC-5 cells in triplicate. Untransfected (N/A) cells and cells transfected with Lipofectamine 2000 alone (Lipo2K) served as negative controls. The numbers shown are the mean and standard deviations of the mean of the indicated cytokine mRNAs relative to the untransfected control and normalized to GAPDH. ( b, c ) In vivo analysis. CD1 ICR mice were administered 2.5 mg/kg LNP-formulated sshRNA (SG220) or LNP-formulated control siRNAs (LUC-U/U, LUC) by intravenous injection. At the designated time point, blood was collected by cardiac puncture and processed as plasma for cytokine determination, and liver was excised and placed in RNAlater (Sigma–Aldrich) for IFIT1 mRNA analysis. The values shown are mean and standard deviation of measurements from each group of four mice. ( b ) Plasma cytokines (left) and liver IFIT mRNA (right), determined 4 hours after administration. ( c ) Time course of SG220-mediated plasma cytokine (left) and liver IFIT1 mRNA (right) induction. LNP, lipid nanoparticles.

    Article Snippet: Cohorts of n = 2 mice were sacrificed at 1 and 48 hours and livers were collected and sliced, and the slices were immersed in RNAlater solution (Ambion, cat#AM7024) overnight at 4 °C.

    Techniques: In Vitro, In Vivo, Transfection, Mouse Assay, Injection, Standard Deviation

    Distribution of biochemical properties of identified proteins. A) molecular weight (kDa) B) isoelectric point C) number of predicted transmembrane helices. Bars represent the proportion (%) of identified proteins belonging in each range. E = ethanol; FF = flash-freezing; R = RNAlater; RF = RNAlater and flash-freezing; N = NAP buffer; AN = autoclaved NAP buffer.

    Journal: bioRxiv

    Article Title: Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes

    doi: 10.1101/2021.07.20.453169

    Figure Lengend Snippet: Distribution of biochemical properties of identified proteins. A) molecular weight (kDa) B) isoelectric point C) number of predicted transmembrane helices. Bars represent the proportion (%) of identified proteins belonging in each range. E = ethanol; FF = flash-freezing; R = RNAlater; RF = RNAlater and flash-freezing; N = NAP buffer; AN = autoclaved NAP buffer.

    Article Snippet: In our study, we immersed samples in RNAlater™ (Invitrogen) in a 1:10 sample: solution ratio and then stored them at room temperature (~22° C) in the dark.

    Techniques: Molecular Weight

    There were no significant differences in total numbers of PSMs, peptides, proteins, and protein groups between samples co-extracted after 1 week of preservation and only minimal differences existed in samples co-extracted after 4 weeks. FF = Flash-freezing, R = RNAlater, RF = RNAlater + flash freezing, N = NAP buffer, AN = Autoclaved NAP buffer, E = 95% Ethanol. 1 week = preserved for one week and first extraction batch. 4 weeks = preserved for 4 weeks and second extraction batch. Bars represent the arithmetic mean (n = 4 for all except E - 4 weeks where n = 3). Error bars represent standard deviation. Asterisks indicate statistical significance (t-test, p-value

    Journal: bioRxiv

    Article Title: Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes

    doi: 10.1101/2021.07.20.453169

    Figure Lengend Snippet: There were no significant differences in total numbers of PSMs, peptides, proteins, and protein groups between samples co-extracted after 1 week of preservation and only minimal differences existed in samples co-extracted after 4 weeks. FF = Flash-freezing, R = RNAlater, RF = RNAlater + flash freezing, N = NAP buffer, AN = Autoclaved NAP buffer, E = 95% Ethanol. 1 week = preserved for one week and first extraction batch. 4 weeks = preserved for 4 weeks and second extraction batch. Bars represent the arithmetic mean (n = 4 for all except E - 4 weeks where n = 3). Error bars represent standard deviation. Asterisks indicate statistical significance (t-test, p-value

    Article Snippet: In our study, we immersed samples in RNAlater™ (Invitrogen) in a 1:10 sample: solution ratio and then stored them at room temperature (~22° C) in the dark.

    Techniques: Preserving, Standard Deviation, T-Test

    High quality RNA can be extracted from cells stored in a solution containing EDTA at 4°C for one week. A) Cartoon of protocol followed to preserved cells in solution. B) Representative 1% agarose gel with RNA from freshly harvested cells and compared with RNA from cells stored in RNAlater, PBS, PBS +, Tre +, and BSA +. Red arrows denote 28S, 18S, and 5S. C) Box plot depicting range of RNA concentrations, center bar indicates median. * denotes p

    Journal: bioRxiv

    Article Title: A low-cost and easy-to-use cell preservation reagent for 4°C or room temperature sample storage

    doi: 10.1101/745232

    Figure Lengend Snippet: High quality RNA can be extracted from cells stored in a solution containing EDTA at 4°C for one week. A) Cartoon of protocol followed to preserved cells in solution. B) Representative 1% agarose gel with RNA from freshly harvested cells and compared with RNA from cells stored in RNAlater, PBS, PBS +, Tre +, and BSA +. Red arrows denote 28S, 18S, and 5S. C) Box plot depicting range of RNA concentrations, center bar indicates median. * denotes p

    Article Snippet: ResultsThe preservation capability of each of the four reagents, PBS, PBS+, Tre+, BSA+, as well as a commercial reagent, RNAlater (Ambion Thermo Fisher, Waltham, MA), were compared to RNA isolated from freshly harvested cells to determine how well RNA is preserved for one week at 4°C.

    Techniques: Agarose Gel Electrophoresis