mouse samples total rna Search Results


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  • 99
    Thermo Fisher mouse liver samples total rna
    Mouse Liver Samples Total Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    mice  (TaKaRa)
    93
    TaKaRa mice
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    TaKaRa mouse organs
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    99
    Thermo Fisher rna
    Decay of the quality of PLT <t>RNA.</t> In another series of experiments, washed PLTs from DT-treated mice were resuspended in Tyrode’s albumin/DMEM medium and incubated at 37°C for 0, 2, 4, 6 and 24h. At the end of each time interval the percentage of TO bright PLTs was determined by FC, after which PLT RNA was extracted in <t>Trizol</t> reagent containing MS2 genomic RNA (see methods ) (n = 4). (A) The profiles of extracted RNAs were analyzed on a Bioanalyzer; a representative series of profiles is shown. Y-axis scales (fluorescence units) are identical for all the electropherograms (20 FU per subdivision). The asterisks indicate the position of MS2 RNA and the right electropherogram corresponds to pure MS2 RNA. First number, time; second number, percentage of TO bright PLTs; third number, 28S/18S RNA ratio; fourth number, percentage of remaining PLT RNA. (B) The decays of rRNA and beta actin mRNA were analyzed by RT-qPCR (see details in method section). Representative amplification curves for MS2, 28S rRNA and beta actin cDNAs at time 0 are shown (1/50 diluted samples, triplicates). No specific amplification products were generated in control experiments without reverse transcriptase (not shown). The relative normalized expression of 28S rRNA and of beta actin mRNA relatively to time 0 were calculated as described in the method section. Histograms represent means and SEM from the 4 independent experiments. C) The presence of beta actin and ubiquitin C transcripts in freshly isolated control and reticulated PLTs was assessed using RNAscope technique. The stringency of the conditions was checked using B subtilis -specific DapB mRNA probes. Hybridized probes were revealed using alkaline phosphatase and HD-assay RED reagent. PLTs were then counterstained with A488-conjugated anti-GP1bβ mAb and DAPI. Upper panels, retPLTs (left, DT) and control PLTs (right, WT) labelled with actin mRNA-specific probes. The masking effect of RED reagent-derived large precipitates on anti-GP1bβ staining is illustrated by arrows. Lower left panel, retPLTs labelled with negative control DapB probes. Lower right panel, retPLTs were stained with Ubiquitin C-specific probes. DAPI staining is not shown because no cells were labelled in the chosen views. Scale bar: 10 μm.
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    88
    Becton Dickinson mouse universal reference total rna
    Decay of the quality of PLT <t>RNA.</t> In another series of experiments, washed PLTs from DT-treated mice were resuspended in Tyrode’s albumin/DMEM medium and incubated at 37°C for 0, 2, 4, 6 and 24h. At the end of each time interval the percentage of TO bright PLTs was determined by FC, after which PLT RNA was extracted in <t>Trizol</t> reagent containing MS2 genomic RNA (see methods ) (n = 4). (A) The profiles of extracted RNAs were analyzed on a Bioanalyzer; a representative series of profiles is shown. Y-axis scales (fluorescence units) are identical for all the electropherograms (20 FU per subdivision). The asterisks indicate the position of MS2 RNA and the right electropherogram corresponds to pure MS2 RNA. First number, time; second number, percentage of TO bright PLTs; third number, 28S/18S RNA ratio; fourth number, percentage of remaining PLT RNA. (B) The decays of rRNA and beta actin mRNA were analyzed by RT-qPCR (see details in method section). Representative amplification curves for MS2, 28S rRNA and beta actin cDNAs at time 0 are shown (1/50 diluted samples, triplicates). No specific amplification products were generated in control experiments without reverse transcriptase (not shown). The relative normalized expression of 28S rRNA and of beta actin mRNA relatively to time 0 were calculated as described in the method section. Histograms represent means and SEM from the 4 independent experiments. C) The presence of beta actin and ubiquitin C transcripts in freshly isolated control and reticulated PLTs was assessed using RNAscope technique. The stringency of the conditions was checked using B subtilis -specific DapB mRNA probes. Hybridized probes were revealed using alkaline phosphatase and HD-assay RED reagent. PLTs were then counterstained with A488-conjugated anti-GP1bβ mAb and DAPI. Upper panels, retPLTs (left, DT) and control PLTs (right, WT) labelled with actin mRNA-specific probes. The masking effect of RED reagent-derived large precipitates on anti-GP1bβ staining is illustrated by arrows. Lower left panel, retPLTs labelled with negative control DapB probes. Lower right panel, retPLTs were stained with Ubiquitin C-specific probes. DAPI staining is not shown because no cells were labelled in the chosen views. Scale bar: 10 μm.
    Mouse Universal Reference Total Rna, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 88/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Stratagene universal mouse reference total rna
    Decay of the quality of PLT <t>RNA.</t> In another series of experiments, washed PLTs from DT-treated mice were resuspended in Tyrode’s albumin/DMEM medium and incubated at 37°C for 0, 2, 4, 6 and 24h. At the end of each time interval the percentage of TO bright PLTs was determined by FC, after which PLT RNA was extracted in <t>Trizol</t> reagent containing MS2 genomic RNA (see methods ) (n = 4). (A) The profiles of extracted RNAs were analyzed on a Bioanalyzer; a representative series of profiles is shown. Y-axis scales (fluorescence units) are identical for all the electropherograms (20 FU per subdivision). The asterisks indicate the position of MS2 RNA and the right electropherogram corresponds to pure MS2 RNA. First number, time; second number, percentage of TO bright PLTs; third number, 28S/18S RNA ratio; fourth number, percentage of remaining PLT RNA. (B) The decays of rRNA and beta actin mRNA were analyzed by RT-qPCR (see details in method section). Representative amplification curves for MS2, 28S rRNA and beta actin cDNAs at time 0 are shown (1/50 diluted samples, triplicates). No specific amplification products were generated in control experiments without reverse transcriptase (not shown). The relative normalized expression of 28S rRNA and of beta actin mRNA relatively to time 0 were calculated as described in the method section. Histograms represent means and SEM from the 4 independent experiments. C) The presence of beta actin and ubiquitin C transcripts in freshly isolated control and reticulated PLTs was assessed using RNAscope technique. The stringency of the conditions was checked using B subtilis -specific DapB mRNA probes. Hybridized probes were revealed using alkaline phosphatase and HD-assay RED reagent. PLTs were then counterstained with A488-conjugated anti-GP1bβ mAb and DAPI. Upper panels, retPLTs (left, DT) and control PLTs (right, WT) labelled with actin mRNA-specific probes. The masking effect of RED reagent-derived large precipitates on anti-GP1bβ staining is illustrated by arrows. Lower left panel, retPLTs labelled with negative control DapB probes. Lower right panel, retPLTs were stained with Ubiquitin C-specific probes. DAPI staining is not shown because no cells were labelled in the chosen views. Scale bar: 10 μm.
    Universal Mouse Reference Total Rna, supplied by Stratagene, used in various techniques. Bioz Stars score: 85/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    TaKaRa mouse testis rna
    Expression of mSgy and <t>mTEAD-2</t> mRNA in established mouse cell lines. Blotting–hybridization analysis of <t>RNA</t> isolated from F9, TM3, TM4 and EL4 mouse cell lines was compared directly with the same sample of mouse testis RNA used in Figure 7B, as described in Figure 7. Each lane contained 20 µg total RNA from the indicated cell line, and 2 µg total RNA from testis. The blank lane contained no RNA.
    Mouse Testis Rna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa mouse colon tissues
    Expression of mSgy and <t>mTEAD-2</t> mRNA in established mouse cell lines. Blotting–hybridization analysis of <t>RNA</t> isolated from F9, TM3, TM4 and EL4 mouse cell lines was compared directly with the same sample of mouse testis RNA used in Figure 7B, as described in Figure 7. Each lane contained 20 µg total RNA from the indicated cell line, and 2 µg total RNA from testis. The blank lane contained no RNA.
    Mouse Colon Tissues, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc truseq stranded total rna sample preparation kits
    Benchmark dataset . A) Three datasets (20TS, 40TS, 80TS), based on spike-in of <t>TruSeq</t> (input: 100 ng total <t>RNA)</t> reads extracted respectively from 20, 40 and 80 million reads were generated using a common background made by 5 different TruSeq library preps having as input 100 ng total RNA (T) and 5 different TruSeq library preps having as input 1000 ng total RNA (C). B) Three datasets (20NU, 40NU, 80NU), based on spike-in of NuGEN (input: 2 ng total RNA) reads extracted respectively from 20, 40 and 80 million reads were generated using the common background described above. Synthetic spikes-in are present both in A and B.
    Truseq Stranded Total Rna Sample Preparation Kits, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 179 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseq stranded total rna sample preparation kit
    Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total <t>RNA</t> was collected and used to synthesize stranded cDNA libraries using the Illumina <t>TruSeq</t> Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.
    Truseq Stranded Total Rna Sample Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1202 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Stratagene total rna control samples
    Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total <t>RNA</t> was collected and used to synthesize stranded cDNA libraries using the Illumina <t>TruSeq</t> Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.
    Total Rna Control Samples, supplied by Stratagene, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Incyte frozen total rna samples
    Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total <t>RNA</t> was collected and used to synthesize stranded cDNA libraries using the Illumina <t>TruSeq</t> Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.
    Frozen Total Rna Samples, supplied by Incyte, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Becton Dickinson mouse control total rna
    Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total <t>RNA</t> was collected and used to synthesize stranded cDNA libraries using the Illumina <t>TruSeq</t> Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.
    Mouse Control Total Rna, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseq stranded total rna sample prep kit
    Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total <t>RNA</t> was collected and used to synthesize stranded cDNA libraries using the Illumina <t>TruSeq</t> Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.
    Truseq Stranded Total Rna Sample Prep Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 943 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa cell culture mouse total skeletal muscle rna
    Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total <t>RNA</t> was collected and used to synthesize stranded cDNA libraries using the Illumina <t>TruSeq</t> Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.
    Cell Culture Mouse Total Skeletal Muscle Rna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Decay of the quality of PLT RNA. In another series of experiments, washed PLTs from DT-treated mice were resuspended in Tyrode’s albumin/DMEM medium and incubated at 37°C for 0, 2, 4, 6 and 24h. At the end of each time interval the percentage of TO bright PLTs was determined by FC, after which PLT RNA was extracted in Trizol reagent containing MS2 genomic RNA (see methods ) (n = 4). (A) The profiles of extracted RNAs were analyzed on a Bioanalyzer; a representative series of profiles is shown. Y-axis scales (fluorescence units) are identical for all the electropherograms (20 FU per subdivision). The asterisks indicate the position of MS2 RNA and the right electropherogram corresponds to pure MS2 RNA. First number, time; second number, percentage of TO bright PLTs; third number, 28S/18S RNA ratio; fourth number, percentage of remaining PLT RNA. (B) The decays of rRNA and beta actin mRNA were analyzed by RT-qPCR (see details in method section). Representative amplification curves for MS2, 28S rRNA and beta actin cDNAs at time 0 are shown (1/50 diluted samples, triplicates). No specific amplification products were generated in control experiments without reverse transcriptase (not shown). The relative normalized expression of 28S rRNA and of beta actin mRNA relatively to time 0 were calculated as described in the method section. Histograms represent means and SEM from the 4 independent experiments. C) The presence of beta actin and ubiquitin C transcripts in freshly isolated control and reticulated PLTs was assessed using RNAscope technique. The stringency of the conditions was checked using B subtilis -specific DapB mRNA probes. Hybridized probes were revealed using alkaline phosphatase and HD-assay RED reagent. PLTs were then counterstained with A488-conjugated anti-GP1bβ mAb and DAPI. Upper panels, retPLTs (left, DT) and control PLTs (right, WT) labelled with actin mRNA-specific probes. The masking effect of RED reagent-derived large precipitates on anti-GP1bβ staining is illustrated by arrows. Lower left panel, retPLTs labelled with negative control DapB probes. Lower right panel, retPLTs were stained with Ubiquitin C-specific probes. DAPI staining is not shown because no cells were labelled in the chosen views. Scale bar: 10 μm.

    Journal: PLoS ONE

    Article Title: Time-Dependent Decay of mRNA and Ribosomal RNA during Platelet Aging and Its Correlation with Translation Activity

    doi: 10.1371/journal.pone.0148064

    Figure Lengend Snippet: Decay of the quality of PLT RNA. In another series of experiments, washed PLTs from DT-treated mice were resuspended in Tyrode’s albumin/DMEM medium and incubated at 37°C for 0, 2, 4, 6 and 24h. At the end of each time interval the percentage of TO bright PLTs was determined by FC, after which PLT RNA was extracted in Trizol reagent containing MS2 genomic RNA (see methods ) (n = 4). (A) The profiles of extracted RNAs were analyzed on a Bioanalyzer; a representative series of profiles is shown. Y-axis scales (fluorescence units) are identical for all the electropherograms (20 FU per subdivision). The asterisks indicate the position of MS2 RNA and the right electropherogram corresponds to pure MS2 RNA. First number, time; second number, percentage of TO bright PLTs; third number, 28S/18S RNA ratio; fourth number, percentage of remaining PLT RNA. (B) The decays of rRNA and beta actin mRNA were analyzed by RT-qPCR (see details in method section). Representative amplification curves for MS2, 28S rRNA and beta actin cDNAs at time 0 are shown (1/50 diluted samples, triplicates). No specific amplification products were generated in control experiments without reverse transcriptase (not shown). The relative normalized expression of 28S rRNA and of beta actin mRNA relatively to time 0 were calculated as described in the method section. Histograms represent means and SEM from the 4 independent experiments. C) The presence of beta actin and ubiquitin C transcripts in freshly isolated control and reticulated PLTs was assessed using RNAscope technique. The stringency of the conditions was checked using B subtilis -specific DapB mRNA probes. Hybridized probes were revealed using alkaline phosphatase and HD-assay RED reagent. PLTs were then counterstained with A488-conjugated anti-GP1bβ mAb and DAPI. Upper panels, retPLTs (left, DT) and control PLTs (right, WT) labelled with actin mRNA-specific probes. The masking effect of RED reagent-derived large precipitates on anti-GP1bβ staining is illustrated by arrows. Lower left panel, retPLTs labelled with negative control DapB probes. Lower right panel, retPLTs were stained with Ubiquitin C-specific probes. DAPI staining is not shown because no cells were labelled in the chosen views. Scale bar: 10 μm.

    Article Snippet: On day 3 of the culture, 80% of the cells were MKs and, RNA was extracted using Trizol reagent and quantified on a Nanodrop spectrophotometer.

    Techniques: Mouse Assay, Incubation, Fluorescence, Quantitative RT-PCR, Amplification, Generated, Expressing, Isolation, HD Assay, Derivative Assay, Staining, Negative Control

    Expression of mSgy and mTEAD-2 mRNA in established mouse cell lines. Blotting–hybridization analysis of RNA isolated from F9, TM3, TM4 and EL4 mouse cell lines was compared directly with the same sample of mouse testis RNA used in Figure 7B, as described in Figure 7. Each lane contained 20 µg total RNA from the indicated cell line, and 2 µg total RNA from testis. The blank lane contained no RNA.

    Journal: Nucleic Acids Research

    Article Title: Soggy, a spermatocyte-specific gene, lies 3.8 kb upstream of and antipodal to TEAD-2, a transcription factor expressed at the beginning of mouse development

    doi:

    Figure Lengend Snippet: Expression of mSgy and mTEAD-2 mRNA in established mouse cell lines. Blotting–hybridization analysis of RNA isolated from F9, TM3, TM4 and EL4 mouse cell lines was compared directly with the same sample of mouse testis RNA used in Figure 7B, as described in Figure 7. Each lane contained 20 µg total RNA from the indicated cell line, and 2 µg total RNA from testis. The blank lane contained no RNA.

    Article Snippet: However, the amount of mTEAD-2 RNA in a sample of mouse testis RNA purchased from Clontech was ∼10-fold less (Fig. B).

    Techniques: Expressing, Hybridization, Isolation

    Expression of mTEAD-2 RNA in the cells of adult mouse testis. In situ RNA:RNA hybridization of sections through adult mouse testis was carried out using 35 S-labeled antisense ( A , C and E ) or sense ( B , D and F ) RNA probes specific for mTEAD-2 mRNA (described in ref. 4) as described in Figure 9.

    Journal: Nucleic Acids Research

    Article Title: Soggy, a spermatocyte-specific gene, lies 3.8 kb upstream of and antipodal to TEAD-2, a transcription factor expressed at the beginning of mouse development

    doi:

    Figure Lengend Snippet: Expression of mTEAD-2 RNA in the cells of adult mouse testis. In situ RNA:RNA hybridization of sections through adult mouse testis was carried out using 35 S-labeled antisense ( A , C and E ) or sense ( B , D and F ) RNA probes specific for mTEAD-2 mRNA (described in ref. 4) as described in Figure 9.

    Article Snippet: However, the amount of mTEAD-2 RNA in a sample of mouse testis RNA purchased from Clontech was ∼10-fold less (Fig. B).

    Techniques: Expressing, In Situ, Hybridization, Labeling

    Expression of mSgy and mTEAD-2 mRNA in mouse adult tissues and embryos. RNA from the indicated mouse tissue was fractionated by gel electrophoresis, transferred to a membrane and then hybridized with the indicated probe ( mSgy , mTEAD-2 or β -actin ). Blots were probed first with the mSgy probe and then stripped and reprobed with the mTEAD-2 probe and then with the β -actin probe. Each sample in ( A ), ( B ) and ( D ) contained 2 µg poly(A) + RNA. Each sample in ( C ) contained 20 µg total RNA. Uterus, ovary, day 9 and day 10 RNA samples were prepared as previously described (4,5). Mouse tissue RNAs in (A) are Clontech MTN Blot no. 7762-1. Mouse 11, 15 and 17 day embryo RNAs in (D) are Clontech MTN Blot no. 7763-1. Mouse testis RNA in (B) was purchased from Clontech (no. 6612-1).

    Journal: Nucleic Acids Research

    Article Title: Soggy, a spermatocyte-specific gene, lies 3.8 kb upstream of and antipodal to TEAD-2, a transcription factor expressed at the beginning of mouse development

    doi:

    Figure Lengend Snippet: Expression of mSgy and mTEAD-2 mRNA in mouse adult tissues and embryos. RNA from the indicated mouse tissue was fractionated by gel electrophoresis, transferred to a membrane and then hybridized with the indicated probe ( mSgy , mTEAD-2 or β -actin ). Blots were probed first with the mSgy probe and then stripped and reprobed with the mTEAD-2 probe and then with the β -actin probe. Each sample in ( A ), ( B ) and ( D ) contained 2 µg poly(A) + RNA. Each sample in ( C ) contained 20 µg total RNA. Uterus, ovary, day 9 and day 10 RNA samples were prepared as previously described (4,5). Mouse tissue RNAs in (A) are Clontech MTN Blot no. 7762-1. Mouse 11, 15 and 17 day embryo RNAs in (D) are Clontech MTN Blot no. 7763-1. Mouse testis RNA in (B) was purchased from Clontech (no. 6612-1).

    Article Snippet: However, the amount of mTEAD-2 RNA in a sample of mouse testis RNA purchased from Clontech was ∼10-fold less (Fig. B).

    Techniques: Expressing, Nucleic Acid Electrophoresis

    Benchmark dataset . A) Three datasets (20TS, 40TS, 80TS), based on spike-in of TruSeq (input: 100 ng total RNA) reads extracted respectively from 20, 40 and 80 million reads were generated using a common background made by 5 different TruSeq library preps having as input 100 ng total RNA (T) and 5 different TruSeq library preps having as input 1000 ng total RNA (C). B) Three datasets (20NU, 40NU, 80NU), based on spike-in of NuGEN (input: 2 ng total RNA) reads extracted respectively from 20, 40 and 80 million reads were generated using the common background described above. Synthetic spikes-in are present both in A and B.

    Journal: BMC Bioinformatics

    Article Title: Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis

    doi: 10.1186/1471-2105-16-S9-S2

    Figure Lengend Snippet: Benchmark dataset . A) Three datasets (20TS, 40TS, 80TS), based on spike-in of TruSeq (input: 100 ng total RNA) reads extracted respectively from 20, 40 and 80 million reads were generated using a common background made by 5 different TruSeq library preps having as input 100 ng total RNA (T) and 5 different TruSeq library preps having as input 1000 ng total RNA (C). B) Three datasets (20NU, 40NU, 80NU), based on spike-in of NuGEN (input: 2 ng total RNA) reads extracted respectively from 20, 40 and 80 million reads were generated using the common background described above. Synthetic spikes-in are present both in A and B.

    Article Snippet: Illumina TruSeq Stranded Total RNA Illumina TruSeq Stranded Total RNA Sample Preparation kit (Low Sample Protocol) was used with slight modifications.

    Techniques: Generated

    Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total RNA was collected and used to synthesize stranded cDNA libraries using the Illumina TruSeq Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.

    Journal: PLoS Pathogens

    Article Title: Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing

    doi: 10.1371/journal.ppat.1005166

    Figure Lengend Snippet: Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total RNA was collected and used to synthesize stranded cDNA libraries using the Illumina TruSeq Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.

    Article Snippet: Total RNA was harvested at 12, 18, 24, and 36-hours post infection from three biological replicates for each condition and was used in the synthesis of stranded cDNA sequencing libraries using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit.

    Techniques: Flow Cytometry, Infection, Blocking Assay