rneasy ffpe kit (Qiagen)

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RNeasy FFPE Kit

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For purification of total RNA from formalin fixed paraffin embedded tissue sections Kit contents Qiagen RNeasy FFPE Kit 50 preps 14 to 30L Elution Volume FFPE Tissue Sample Total RNA Purification Spin Column Format Silica Technology Ideal for PCR qPCR Real time RT PCR Microarray Includes 50 RNeasy MinElute Spin Columns Collection Tubes Proteinase K RNase free DNase I DNase Booster Buffer RNase free Buffers RNase free Water Benefits Novel method to overcome formalin crosslinking Efficient release of RNA without compromising integrity Streamlined protocol providing RNA in just 85 minu

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73504

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445

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RNeasy FFPE Kit

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Qiagen rneasy ffpe kit

rneasy ffpe kit - by Bioz Stars, 2021-02

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1) Product Images from "Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?"

Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?

Journal: BMC Clinical Pathology

doi: 10.1186/s12907-016-0039-3

Investigating the relationship between RNA concentration and the input amount of tissue: Geometric mean increase in RNA concentration ( n = 6) when combining 5 μm sections in a linear fashion and associated standard error of mean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE kit, b Qiagen RNeasy, c Arcturus Paradise plus FFPE RNA isolation kit, d Maxwell 16 LEV RNA FFPE Purification kit

Figure Legend Snippet: Investigating the relationship between RNA concentration and the input amount of tissue: Geometric mean increase in RNA concentration ( n = 6) when combining 5 μm sections in a linear fashion and associated standard error of mean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE kit, b Qiagen RNeasy, c Arcturus Paradise plus FFPE RNA isolation kit, d Maxwell 16 LEV RNA FFPE Purification kit

Techniques Used: Concentration Assay, Formalin-fixed Paraffin-Embedded, Isolation, Purification

2) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

Figure Legend Snippet: Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

3) Product Images from "Clearance of Chikungunya Virus Infection in Lymphoid Tissues Is Promoted by Treatment with an Agonistic Anti-CD137 Antibody"

Article Title: Clearance of Chikungunya Virus Infection in Lymphoid Tissues Is Promoted by Treatment with an Agonistic Anti-CD137 Antibody

Journal: Journal of Virology

doi: 10.1128/JVI.01231-19

Germinal center (GC) B cells and FDCs harbor CHIKV viral RNA. Four-week-old WT C57BL/6 male mice were inoculated with 10 3 FFU of CHIKV-LR. At 2 dpi, 400 μg of agonistic anti-CD137 MAb or isotype-control MAb was administered via the i.p. route. (A) Spleens were harvested at 7 dpi, and viral RNA (brown) was visualized by ISH. Tissue sections were counterstained with Gill’s hematoxylin. Scale bars, 50 μm. (B) Insets of panel A (black boxes) visualized at higher magnification. Scale bars, 10 μm. Yellow arrows indicate CHIKV RNA. (C) Spleens were harvested at 7 dpi (left) or 14 dpi (right), and bulk cells were fixed with PFA and sorted using flow cytometry. Viral RNA in each sorted cell subset was measured by qRT-PCR and normalized to 18S. (D to F) Four-week-old WT C57BL/6 male mice were inoculated with 10 3 PFU of CHIKV SL15649. Spleens were harvested at 3, 7, and 14 dpi, CHIKV E1 (D) and nsP2 (E) RNA from tissue homogenates was measured by qRT-PCR, and the ratio of E1 RNA to nsP2 RNA was calculated (F). Data were pooled from two experiments. Each symbol represents one mouse, and bars indicate median values. *, P

Figure Legend Snippet: Germinal center (GC) B cells and FDCs harbor CHIKV viral RNA. Four-week-old WT C57BL/6 male mice were inoculated with 10 3 FFU of CHIKV-LR. At 2 dpi, 400 μg of agonistic anti-CD137 MAb or isotype-control MAb was administered via the i.p. route. (A) Spleens were harvested at 7 dpi, and viral RNA (brown) was visualized by ISH. Tissue sections were counterstained with Gill’s hematoxylin. Scale bars, 50 μm. (B) Insets of panel A (black boxes) visualized at higher magnification. Scale bars, 10 μm. Yellow arrows indicate CHIKV RNA. (C) Spleens were harvested at 7 dpi (left) or 14 dpi (right), and bulk cells were fixed with PFA and sorted using flow cytometry. Viral RNA in each sorted cell subset was measured by qRT-PCR and normalized to 18S. (D to F) Four-week-old WT C57BL/6 male mice were inoculated with 10 3 PFU of CHIKV SL15649. Spleens were harvested at 3, 7, and 14 dpi, CHIKV E1 (D) and nsP2 (E) RNA from tissue homogenates was measured by qRT-PCR, and the ratio of E1 RNA to nsP2 RNA was calculated (F). Data were pooled from two experiments. Each symbol represents one mouse, and bars indicate median values. *, P

Techniques Used: Mouse Assay, In Situ Hybridization, Flow Cytometry, Quantitative RT-PCR

4) Product Images from "Clearance of Chikungunya Virus Infection in Lymphoid Tissues Is Promoted by Treatment with an Agonistic Anti-CD137 Antibody"

Article Title: Clearance of Chikungunya Virus Infection in Lymphoid Tissues Is Promoted by Treatment with an Agonistic Anti-CD137 Antibody

Journal: Journal of Virology

doi: 10.1128/JVI.01231-19

Techniques Used: Mouse Assay, In Situ Hybridization, Flow Cytometry, Quantitative RT-PCR

5) Product Images from "Phosphorylated TDP-43 (pTDP-43) aggregates in the axial skeletal muscle of patients with sporadic and familial amyotrophic lateral sclerosis"

Article Title: Phosphorylated TDP-43 (pTDP-43) aggregates in the axial skeletal muscle of patients with sporadic and familial amyotrophic lateral sclerosis

Journal: Acta Neuropathologica Communications

doi: 10.1186/s40478-018-0528-y

). Three non-ALS, non-IBM samples with mild neurogenic atrophy in the muscle biopsy were also studied (“MSC1–3”). SQSTM1 and TARDBP were analyzed relative to the expression of two housekeeping genes ( 18 s , GAPDH ) and data shown are combined from two 96-well plates (4 replicates per sample and primer). There was a significant increase in relative normalized gene expression for both ALS and IBM samples ( a ), relative to controls (right) and this was most significant for SQSTM1 expression in ALS samples ( > 4-fold expression relative to controls, P

Figure Legend Snippet: ). Three non-ALS, non-IBM samples with mild neurogenic atrophy in the muscle biopsy were also studied (“MSC1–3”). SQSTM1 and TARDBP were analyzed relative to the expression of two housekeeping genes ( 18 s , GAPDH ) and data shown are combined from two 96-well plates (4 replicates per sample and primer). There was a significant increase in relative normalized gene expression for both ALS and IBM samples ( a ), relative to controls (right) and this was most significant for SQSTM1 expression in ALS samples ( > 4-fold expression relative to controls, P

Techniques Used: Expressing

6) Product Images from "Bromodomain Protein BRD4 Is a Transcriptional Repressor of Autophagy and Lysosomal Function"

Article Title: Bromodomain Protein BRD4 Is a Transcriptional Repressor of Autophagy and Lysosomal Function

Journal: Molecular Cell

doi: 10.1016/j.molcel.2017.04.027

Starvation Leads to BRD4 Dissociation from Autophagy Gene Promoters (A and B) KP-4 cells were starved for 4 hr followed by chromatin immunoprecipitation (ChIP) assay with BRD4 antibody (A) and RT-qPCR analysis (B). (C) KP-4 cells infected with Cas9/hMOF sgRNA were subjected to ChIP assay with BRD4 antibody. (D) KP-4 cells were starved for 4 hr followed by ChIP assay with H4K16Ac antibody. (E and F) KP-4 cells infected with Cas9/SIRT1 sgRNA were starved for 4 hr followed by ChIP assay with BRD4 antibody (E) and RT-qPCR analysis (F). Western blot shows efficient SIRT1 depletion in Cas9/SIRT1 sgRNA-infected cells. (G and H) KP-4 cells infected with Cas9/AMPKα1 and α2 sgRNAs were starved for 4 hr followed by immunoprecipitation with DBC1 antibody (G) and RT-qPCR analysis (H). All data are shown as mean ± SD. In (A)–(F) and (H), n = 3 independent experiments. ∗ p

Figure Legend Snippet: Starvation Leads to BRD4 Dissociation from Autophagy Gene Promoters (A and B) KP-4 cells were starved for 4 hr followed by chromatin immunoprecipitation (ChIP) assay with BRD4 antibody (A) and RT-qPCR analysis (B). (C) KP-4 cells infected with Cas9/hMOF sgRNA were subjected to ChIP assay with BRD4 antibody. (D) KP-4 cells were starved for 4 hr followed by ChIP assay with H4K16Ac antibody. (E and F) KP-4 cells infected with Cas9/SIRT1 sgRNA were starved for 4 hr followed by ChIP assay with BRD4 antibody (E) and RT-qPCR analysis (F). Western blot shows efficient SIRT1 depletion in Cas9/SIRT1 sgRNA-infected cells. (G and H) KP-4 cells infected with Cas9/AMPKα1 and α2 sgRNAs were starved for 4 hr followed by immunoprecipitation with DBC1 antibody (G) and RT-qPCR analysis (H). All data are shown as mean ± SD. In (A)–(F) and (H), n = 3 independent experiments. ∗ p

Techniques Used: Chromatin Immunoprecipitation, Quantitative RT-PCR, Infection, Western Blot, Immunoprecipitation

BRD4 Represses Autophagy Gene Expression through G9a (A) Cell extracts from KP-4 cells were subjected to immunoprecipitation with G9a (upper) and BRD4 (lower) antibodies. (B) KP-4 cells were starved for 4 hr followed by immunoprecipitation with BRD4 antibody. (C–F) KP-4 cells were treated with 500 nM JQ1 for 9 hr (C and E). KP-4 cells harboring inducible control or BRD4 shRNA were treated with 500 ng/mL doxycycline (DOX) for 4 days (D and F). ChIP assays were performed using G9a (C and D) and H3K9diMe (E and F) antibodies. (G and H) KP-4 cells infected with shRNA targeting G9a were transfected with BRD4 siRNA followed by RT-qPCR (G) and western blot (H). (I) KP-4 cells overexpressing BRD4 were infected with shRNA targeting G9a. All data are shown as mean ± SD. In (C)–(G), n = 3 independent experiments. ∗ p

Figure Legend Snippet: BRD4 Represses Autophagy Gene Expression through G9a (A) Cell extracts from KP-4 cells were subjected to immunoprecipitation with G9a (upper) and BRD4 (lower) antibodies. (B) KP-4 cells were starved for 4 hr followed by immunoprecipitation with BRD4 antibody. (C–F) KP-4 cells were treated with 500 nM JQ1 for 9 hr (C and E). KP-4 cells harboring inducible control or BRD4 shRNA were treated with 500 ng/mL doxycycline (DOX) for 4 days (D and F). ChIP assays were performed using G9a (C and D) and H3K9diMe (E and F) antibodies. (G and H) KP-4 cells infected with shRNA targeting G9a were transfected with BRD4 siRNA followed by RT-qPCR (G) and western blot (H). (I) KP-4 cells overexpressing BRD4 were infected with shRNA targeting G9a. All data are shown as mean ± SD. In (C)–(G), n = 3 independent experiments. ∗ p

Techniques Used: Expressing, Immunoprecipitation, shRNA, Chromatin Immunoprecipitation, Infection, Transfection, Quantitative RT-PCR, Western Blot

BRD4 Is a Negative Regulator of Autophagy Gene Expression (A and B) KP-4 cells transfected with control or BRD4 siRNA were subjected to RNA-seq and gene ontology analyses (A) and RT-qPCR analysis (B). (C) RT-qPCR analysis of KP-4 cells treated with DMSO, 500 nM JQ1, 500 nM I-BET151, or 500 nM OTX015 for 9 hr. (D) RT-qPCR analysis of KP-4 cells treated with 500 nM JQ1 for the indicated time. (E) RT-qPCR analysis of KP-4 cells overexpressing BRD4. All data are shown as mean ± SD. In (A)–(D), n = 3 independent experiments; in (E), data are representative of two independent experiments performed in triplicate. ∗ p

Figure Legend Snippet: BRD4 Is a Negative Regulator of Autophagy Gene Expression (A and B) KP-4 cells transfected with control or BRD4 siRNA were subjected to RNA-seq and gene ontology analyses (A) and RT-qPCR analysis (B). (C) RT-qPCR analysis of KP-4 cells treated with DMSO, 500 nM JQ1, 500 nM I-BET151, or 500 nM OTX015 for 9 hr. (D) RT-qPCR analysis of KP-4 cells treated with 500 nM JQ1 for the indicated time. (E) RT-qPCR analysis of KP-4 cells overexpressing BRD4. All data are shown as mean ± SD. In (A)–(D), n = 3 independent experiments; in (E), data are representative of two independent experiments performed in triplicate. ∗ p

Techniques Used: Expressing, Transfection, RNA Sequencing Assay, Quantitative RT-PCR

BRD4 Knockdown Sustains mTOR Activity during Starvation and Confers Resistance to Starvation-Induced Cell Death (A and B) KP-4 cells transfected with BRD4 siRNA were starved of amino acids (A). Cells pre-treated with CQ (10 μM, 4 hr) were subjected to amino acid starvation for 2 hr in the presence of CQ (B). (C) KP-4 cells infected with Cas9/ATG5 sgRNA were transfected with BRD4 siRNA and subjected to amino acid starvation for 2 hr. (D and E) KP-4 cells infected with Cas9/ATG5 sgRNA were transfected with BRD4 siRNA. Following 48 hr starvation, percentage of subG1 cells (D) and cell number (E) were determined (n = 3 independent experiments). (F and G) KP-4 cells transfected with BRD4 siRNA were starved for 48 hr in the presence or absence of 10 μM CQ. Percentage of dead (F) and surviving (G) cells was determined by trypan blue exclusion test (n = 4 independent experiments). All data are shown as mean ± SD. ∗ p

Figure Legend Snippet: BRD4 Knockdown Sustains mTOR Activity during Starvation and Confers Resistance to Starvation-Induced Cell Death (A and B) KP-4 cells transfected with BRD4 siRNA were starved of amino acids (A). Cells pre-treated with CQ (10 μM, 4 hr) were subjected to amino acid starvation for 2 hr in the presence of CQ (B). (C) KP-4 cells infected with Cas9/ATG5 sgRNA were transfected with BRD4 siRNA and subjected to amino acid starvation for 2 hr. (D and E) KP-4 cells infected with Cas9/ATG5 sgRNA were transfected with BRD4 siRNA. Following 48 hr starvation, percentage of subG1 cells (D) and cell number (E) were determined (n = 3 independent experiments). (F and G) KP-4 cells transfected with BRD4 siRNA were starved for 48 hr in the presence or absence of 10 μM CQ. Percentage of dead (F) and surviving (G) cells was determined by trypan blue exclusion test (n = 4 independent experiments). All data are shown as mean ± SD. ∗ p

Techniques Used: Activity Assay, Transfection, Infection

BRD4 Knockdown Enhances Lysosomal Function (A) RT-qPCR analysis of KP-4 cells transfected with control or BRD4 siRNA. (B–D) KP-4 cells transfected with BRD4 siRNA were subjected to western blot analysis with antibodies against lysosomal proteins (B) and stained with LAMP1 antibody (C), LysoTracker Red (100 nM, 2 hr) (D, upper panels), and Magic Red CTSB (1 hr) (D, lower panels). Area of LAMP1 + , LysoTracker + , and Magic Red CTSB + area normalized to cell number is shown (C, CON: n = 115 cells, BRD4: n = 130 cells; D upper, CON: n = 66 cells, BRD4 1: n = 52 cells, BRD4 2: n = 50 cells; D lower, CON: n = 164 cells, BRD4 1: n = 109 cells, BRD4 2: n = 53 cells). Scale bars, 50 μm. (E) Hexosaminidase activity was measured using lysates from control and BRD4 knockdown KP-4 cells. (F and G) RT-qPCR analysis of TY-82 cells transfected with NUT siRNA for 72 hr (F) or treated with 500 nM JQ1 for 9 hr (G). (H) KP-4 cells were transfected with BRD4 and/or MiT/TFE (TFEB, TFE3, MITF) siRNAs and treated with 10 μM CQ for 4 hr. All data are shown as mean ± SD. In (A) and (F), n = 3 independent experiments. In (E), n = 4 independent experiments. In (G), data are representative of two independent experiments performed in triplicate. ∗ p

Figure Legend Snippet: BRD4 Knockdown Enhances Lysosomal Function (A) RT-qPCR analysis of KP-4 cells transfected with control or BRD4 siRNA. (B–D) KP-4 cells transfected with BRD4 siRNA were subjected to western blot analysis with antibodies against lysosomal proteins (B) and stained with LAMP1 antibody (C), LysoTracker Red (100 nM, 2 hr) (D, upper panels), and Magic Red CTSB (1 hr) (D, lower panels). Area of LAMP1 + , LysoTracker + , and Magic Red CTSB + area normalized to cell number is shown (C, CON: n = 115 cells, BRD4: n = 130 cells; D upper, CON: n = 66 cells, BRD4 1: n = 52 cells, BRD4 2: n = 50 cells; D lower, CON: n = 164 cells, BRD4 1: n = 109 cells, BRD4 2: n = 53 cells). Scale bars, 50 μm. (E) Hexosaminidase activity was measured using lysates from control and BRD4 knockdown KP-4 cells. (F and G) RT-qPCR analysis of TY-82 cells transfected with NUT siRNA for 72 hr (F) or treated with 500 nM JQ1 for 9 hr (G). (H) KP-4 cells were transfected with BRD4 and/or MiT/TFE (TFEB, TFE3, MITF) siRNAs and treated with 10 μM CQ for 4 hr. All data are shown as mean ± SD. In (A) and (F), n = 3 independent experiments. In (E), n = 4 independent experiments. In (G), data are representative of two independent experiments performed in triplicate. ∗ p

Techniques Used: Quantitative RT-PCR, Transfection, Western Blot, Staining, Activity Assay

BRD4 Silencing Enhances Autophagic Flux (A) Drosophila S2R + cells expressing GFP-LC3 were transfected with double-stranded RNA (dsRNA) targeting control luciferase (Luc) or Fs(1)h. (B and C) KP-4 cells transfected with control or BRD4 siRNA for 72 hr were subjected to western blot analysis (B) and stained for LC3B (C). The number of LC3 puncta normalized to cell number is shown. CON: n = 94 cells, BRD4 1: n = 97 cells, BRD4 2: n = 74 cells. Scale bars, 50 μm. (D) Immunohistochemistry of small intestinal sections from transgenic mice harboring inducible renilla luciferase or BRD4 shRNA. Sections were stained for LC3 (upper) and BRD4 (lower). Cytoplasmic signal in BRD4 panels is due to non-specific staining. Scale bars, 50 μm. (E) KP-4 cells transfected with BRD4 siRNA were treated with 10 μM CQ for 4 hr. (F) KP-4 cells transfected with BRD4 siRNA were stained for WIPI2. The number of WIPI2 puncta normalized to cell number is shown. CON: n = 119 cells, BRD4 1: n = 107 cells, BRD4 2: n = 109 cells. Scale bars, 20 μm. (G) KP-4 cells stably expressing RFP-GFP-LC3 were transfected with BRD4 siRNA. Scale bars, 50 μm. (H) KP-4 cells were treated with 500 nM JQ1 for 9 hr in the presence or absence of CQ (10 μM, 4 hr). (I) KP-4 cells overexpressing BRD4 were treated with 10 μM CQ for 4 hr. (J) TY-82 cells transfected with NUT siRNA for 5 days were treated with 10 μM CQ for 8 hr. BRD4-NUT was detected using NUT antibody. All data are shown as mean ± SD. ∗ p

Figure Legend Snippet: BRD4 Silencing Enhances Autophagic Flux (A) Drosophila S2R + cells expressing GFP-LC3 were transfected with double-stranded RNA (dsRNA) targeting control luciferase (Luc) or Fs(1)h. (B and C) KP-4 cells transfected with control or BRD4 siRNA for 72 hr were subjected to western blot analysis (B) and stained for LC3B (C). The number of LC3 puncta normalized to cell number is shown. CON: n = 94 cells, BRD4 1: n = 97 cells, BRD4 2: n = 74 cells. Scale bars, 50 μm. (D) Immunohistochemistry of small intestinal sections from transgenic mice harboring inducible renilla luciferase or BRD4 shRNA. Sections were stained for LC3 (upper) and BRD4 (lower). Cytoplasmic signal in BRD4 panels is due to non-specific staining. Scale bars, 50 μm. (E) KP-4 cells transfected with BRD4 siRNA were treated with 10 μM CQ for 4 hr. (F) KP-4 cells transfected with BRD4 siRNA were stained for WIPI2. The number of WIPI2 puncta normalized to cell number is shown. CON: n = 119 cells, BRD4 1: n = 107 cells, BRD4 2: n = 109 cells. Scale bars, 20 μm. (G) KP-4 cells stably expressing RFP-GFP-LC3 were transfected with BRD4 siRNA. Scale bars, 50 μm. (H) KP-4 cells were treated with 500 nM JQ1 for 9 hr in the presence or absence of CQ (10 μM, 4 hr). (I) KP-4 cells overexpressing BRD4 were treated with 10 μM CQ for 4 hr. (J) TY-82 cells transfected with NUT siRNA for 5 days were treated with 10 μM CQ for 8 hr. BRD4-NUT was detected using NUT antibody. All data are shown as mean ± SD. ∗ p

Techniques Used: Expressing, Transfection, Luciferase, Western Blot, Staining, Immunohistochemistry, Transgenic Assay, Mouse Assay, shRNA, Stable Transfection

$Effect of BRD4 Silencing on Stimulus-Dependent and Selective Autophagy (A–F) Cells transfected with BRD4 siRNA were starved for 1–5 hr (KP-4 cells, A), treated with 500 nM rapamycin for 24 hr (KP-4 cells, B), starved of glucose for 4 hr (KP-4 cells, C), cultured under hypoxic (1% O 2 ) conditions for 48 hr (SUIT2 cells, D), treated with 100 mM Trehalose for 4 hr (KP-4 cells, E), or treated with 500 nM 4-Hydroxytamoxifen (4-OHT) for 48 hr (IMR90 ER-HRas G12V cells, F). (G) KP-4 cells harboring rtTA and Tre-tight-HTT Q94-CFP were transfected with BRD4 siRNA. At 12 hr after transfection, cells were treated with 1 μg/mL DOX for 10 hr. At 48 hr after removal of DOX, cells were separated into Triton X-100 soluble and insoluble fractions. (H) KP-4 cells transfected with BRD4 siRNA were infected with Salmonella enterica serovar Typhimurium. The number of Salmonella was determined by performing colony-forming unit assays at 2, 6, and 8 hr after infection and normalized to the numbers at 2 hr. Data are shown as mean ± SEM; n = 4 independent experiments. (I) KP-4 cells expressing YFP-parkin were transfected with BRD4 siRNA followed by treatment with 1 μM Antimycin A and 1 μM Oligomycin for 8 hr. See also Figure S6 .$
Figure Legend Snippet: Effect of BRD4 Silencing on Stimulus-Dependent and Selective Autophagy (A–F) Cells transfected with BRD4 siRNA were starved for 1–5 hr (KP-4 cells, A), treated with 500 nM rapamycin for 24 hr (KP-4 cells, B), starved of glucose for 4 hr (KP-4 cells, C), cultured under hypoxic (1% O 2 ) conditions for 48 hr (SUIT2 cells, D), treated with 100 mM Trehalose for 4 hr (KP-4 cells, E), or treated with 500 nM 4-Hydroxytamoxifen (4-OHT) for 48 hr (IMR90 ER-HRas G12V cells, F). (G) KP-4 cells harboring rtTA and Tre-tight-HTT Q94-CFP were transfected with BRD4 siRNA. At 12 hr after transfection, cells were treated with 1 μg/mL DOX for 10 hr. At 48 hr after removal of DOX, cells were separated into Triton X-100 soluble and insoluble fractions. (H) KP-4 cells transfected with BRD4 siRNA were infected with Salmonella enterica serovar Typhimurium. The number of Salmonella was determined by performing colony-forming unit assays at 2, 6, and 8 hr after infection and normalized to the numbers at 2 hr. Data are shown as mean ± SEM; n = 4 independent experiments. (I) KP-4 cells expressing YFP-parkin were transfected with BRD4 siRNA followed by treatment with 1 μM Antimycin A and 1 μM Oligomycin for 8 hr. See also Figure S6 .

Techniques Used: Transfection, Cell Culture, Infection, Expressing

7) Product Images from "Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue"

Article Title: Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Journal: BMC Cancer

doi: 10.1186/s12885-017-3237-1

TNBC molecular subtype concordance between matched FF and FFPE samples processed on microarray and RNA-seq improves with increased prediction confidence. a Scatterplot shows TNBC subtype accuracy between microarray and RNA-seq as a function of prediction confidence in the TCGA breast (BRCA) cohort. b Plot shows RNA-seq prediction accuracy by confidence score. Vertical line cutoff demarks the prediction confidence score generating 95% concordance between platforms. c Scatterplot shows the concordance between microarray and RNA-seq platforms by strength of correlation to a subtype (prediction score)

Figure Legend Snippet: TNBC molecular subtype concordance between matched FF and FFPE samples processed on microarray and RNA-seq improves with increased prediction confidence. a Scatterplot shows TNBC subtype accuracy between microarray and RNA-seq as a function of prediction confidence in the TCGA breast (BRCA) cohort. b Plot shows RNA-seq prediction accuracy by confidence score. Vertical line cutoff demarks the prediction confidence score generating 95% concordance between platforms. c Scatterplot shows the concordance between microarray and RNA-seq platforms by strength of correlation to a subtype (prediction score)

Techniques Used: Formalin-fixed Paraffin-Embedded, Microarray, RNA Sequencing Assay

MiSeq and HiSeq platform mapped read comparison from FF- and FFPE-derived RNA sequences. a Barplot depicts the percentage of mapped reads that are on-target, or off-target (intronic and intergenic) for FF and FFPE samples processed on MiSeq and HiSeq platforms. b Beeswarm box plot shows mapped reads (%) form individual FF ( blue ) and FFPE ( red ) samples processed on the HiSeq

Figure Legend Snippet: MiSeq and HiSeq platform mapped read comparison from FF- and FFPE-derived RNA sequences. a Barplot depicts the percentage of mapped reads that are on-target, or off-target (intronic and intergenic) for FF and FFPE samples processed on MiSeq and HiSeq platforms. b Beeswarm box plot shows mapped reads (%) form individual FF ( blue ) and FFPE ( red ) samples processed on the HiSeq

Techniques Used: Formalin-fixed Paraffin-Embedded, Derivative Assay

8) Product Images from "CDK1 and CCNB1 as potential diagnostic markers of rhabdomyosarcoma: validation following bioinformatics analysis"

Article Title: CDK1 and CCNB1 as potential diagnostic markers of rhabdomyosarcoma: validation following bioinformatics analysis

Journal: BMC Medical Genomics

doi: 10.1186/s12920-019-0645-x

Validation of 10 hub genes by RT-PCR. mRNA expression levels of 10 hub genes were detected in RMS patient tissue and normal striated muscle tissue. Each point represents an individual subject. * p

Figure Legend Snippet: Validation of 10 hub genes by RT-PCR. mRNA expression levels of 10 hub genes were detected in RMS patient tissue and normal striated muscle tissue. Each point represents an individual subject. * p

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Expressing

9) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

10) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

11) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

12) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

13) Product Images from "Clearance of Chikungunya Virus Infection in Lymphoid Tissues Is Promoted by Treatment with an Agonistic Anti-CD137 Antibody"

Article Title: Clearance of Chikungunya Virus Infection in Lymphoid Tissues Is Promoted by Treatment with an Agonistic Anti-CD137 Antibody

Journal: Journal of Virology

doi: 10.1128/JVI.01231-19

Techniques Used: Mouse Assay, In Situ Hybridization, Flow Cytometry, Quantitative RT-PCR

14) Product Images from "Upregulation of P2Y2R, Active uPA, and PAI-1 Are Essential Components of Hantavirus Cardiopulmonary Syndrome"

Article Title: Upregulation of P2Y2R, Active uPA, and PAI-1 Are Essential Components of Hantavirus Cardiopulmonary Syndrome

Journal: Frontiers in Cellular and Infection Microbiology

doi: 10.3389/fcimb.2018.00169

P2Y 2 R expression is significantly upregulated in HCPS compared to controls. RNA was extracted from lung tissues samples with the Qiagen RNeasy FFPE kit (cat# 73504) and quantified with a Thermo Fisher Scientific Nanodrop. P2Y 2 R expression levels were measured by the TaqMan assay using a WT P2Y 2 R plasmid as standard. P2Y 2 R copy #s were normalized to total RNA extracted from the embedded tissues. Each sample slice was measured in triplicate. (A) The plot of P2Y 2 R for each HCPS patient, shown on the x-axis as H1-H22. Each data point per patient represents a triplicate measurement of P2Y 2 R expression in a 10 μm slice cut from the FFPE blocks. The number of segments analyzed is shown for each case above the replicate data points (e.g., n = 11 for H1). Ninety-seven distinct segments from all cases were analyzed. Lung tissues from two decedents (H4, and H9) were not available. The error bars represent the median and range. For all HCPS samples, the minimum, median, maximum and mean values were 0.0055, 2.10, 24.88, and 4.1 ± 0.48 (SEM). (B,C) Plot of P2Y 2 R for pneumonia (P) and gunshot wound cases (GSW). The experimental conditions are similar to those described for HCPS. Cases for which no lung tissue samples were available were excluded from the graph. For all pneumonia tissue segment samples ( n = 39), the minimum, median, maximum and mean values were 0.0005, 0.07, 4.4, 0.54 ± 0.16. For all GSW samples ( n = 21), the minimum, median, maximum and mean values were 0.0052, 0.18, 2.4, and 0.46 ± 0.10 (SEM).

Figure Legend Snippet: P2Y 2 R expression is significantly upregulated in HCPS compared to controls. RNA was extracted from lung tissues samples with the Qiagen RNeasy FFPE kit (cat# 73504) and quantified with a Thermo Fisher Scientific Nanodrop. P2Y 2 R expression levels were measured by the TaqMan assay using a WT P2Y 2 R plasmid as standard. P2Y 2 R copy #s were normalized to total RNA extracted from the embedded tissues. Each sample slice was measured in triplicate. (A) The plot of P2Y 2 R for each HCPS patient, shown on the x-axis as H1-H22. Each data point per patient represents a triplicate measurement of P2Y 2 R expression in a 10 μm slice cut from the FFPE blocks. The number of segments analyzed is shown for each case above the replicate data points (e.g., n = 11 for H1). Ninety-seven distinct segments from all cases were analyzed. Lung tissues from two decedents (H4, and H9) were not available. The error bars represent the median and range. For all HCPS samples, the minimum, median, maximum and mean values were 0.0055, 2.10, 24.88, and 4.1 ± 0.48 (SEM). (B,C) Plot of P2Y 2 R for pneumonia (P) and gunshot wound cases (GSW). The experimental conditions are similar to those described for HCPS. Cases for which no lung tissue samples were available were excluded from the graph. For all pneumonia tissue segment samples ( n = 39), the minimum, median, maximum and mean values were 0.0005, 0.07, 4.4, 0.54 ± 0.16. For all GSW samples ( n = 21), the minimum, median, maximum and mean values were 0.0052, 0.18, 2.4, and 0.46 ± 0.10 (SEM).

Techniques Used: Expressing, Formalin-fixed Paraffin-Embedded, TaqMan Assay, Plasmid Preparation

15) Product Images from "Felis catus papillomavirus type-2 E6 binds to E6AP, promotes E6AP/p53 binding and enhances p53 proteasomal degradation"

Article Title: Felis catus papillomavirus type-2 E6 binds to E6AP, promotes E6AP/p53 binding and enhances p53 proteasomal degradation

Journal: Scientific Reports

doi: 10.1038/s41598-018-35723-7

FcaPV-2 E6 mRNA levels, expression and localization of p53 and E6AP in feline oral SCC cell lines. ( a ) SCCF2 and SCCF3 cells were subjected to RNA extraction, reverse transcription and Real time quantitative PCR (qPCR) to analyse FcaPV-2 E6 gene expression. Results were normalised for β2-microglobulin expression. The graph shows the results as mean +/− standard deviations (SD) of five independent experiments where the cell line with higher E6 expression levels (SCCF3) (P = 0.0062) was arbitrarily set as calibrator. ( b ) Cells were analysed by Real-time qPCR for p53 gene expression and results normalized as above. The graph represents mean +/− SD from three independent experiment and demonstrates p53 down-regulation in SCCF3 compared to SCCF2 set as calibrator (P = 0.00). Representative WB gels for p53 and E6AP are also shown. Stripping and reprobing with β-actin confirmed equal protein loadings. ( c ) SCCF2 and SCCF3 cells were grown on coverslips and subjected to double IF staining for p53 (green fluorescence) and E6AP (red fluorescence), nuclei were counterstained with DAPI. Representative fields showing nuclear or cytoplasmic/perinuclear p53 expression in SCCF2 and undetectable p53 staining in SCCF3 are illustrated. White arrows indicate perinuclear co-localization (yellow fluorescence) of the two proteins in a sub-set of SCCF2 cells in the merge panel.

Figure Legend Snippet: FcaPV-2 E6 mRNA levels, expression and localization of p53 and E6AP in feline oral SCC cell lines. ( a ) SCCF2 and SCCF3 cells were subjected to RNA extraction, reverse transcription and Real time quantitative PCR (qPCR) to analyse FcaPV-2 E6 gene expression. Results were normalised for β2-microglobulin expression. The graph shows the results as mean +/− standard deviations (SD) of five independent experiments where the cell line with higher E6 expression levels (SCCF3) (P = 0.0062) was arbitrarily set as calibrator. ( b ) Cells were analysed by Real-time qPCR for p53 gene expression and results normalized as above. The graph represents mean +/− SD from three independent experiment and demonstrates p53 down-regulation in SCCF3 compared to SCCF2 set as calibrator (P = 0.00). Representative WB gels for p53 and E6AP are also shown. Stripping and reprobing with β-actin confirmed equal protein loadings. ( c ) SCCF2 and SCCF3 cells were grown on coverslips and subjected to double IF staining for p53 (green fluorescence) and E6AP (red fluorescence), nuclei were counterstained with DAPI. Representative fields showing nuclear or cytoplasmic/perinuclear p53 expression in SCCF2 and undetectable p53 staining in SCCF3 are illustrated. White arrows indicate perinuclear co-localization (yellow fluorescence) of the two proteins in a sub-set of SCCF2 cells in the merge panel.

Techniques Used: Expressing, RNA Extraction, Real-time Polymerase Chain Reaction, Western Blot, Stripping Membranes, Staining, Fluorescence

16) Product Images from "Embryonic Stem Cell-Like Subpopulations in Venous Malformation"

Article Title: Embryonic Stem Cell-Like Subpopulations in Venous Malformation

Journal: Frontiers in Medicine

doi: 10.3389/fmed.2017.00162

3,3′-Diaminobenzidine immunohistochemical-stained images demonstrating the expression of Nanog [ (A,B) , red], pSTAT3 [ (C,D) , brown], OCT4 [ (E,F) , brown], SOX2 [ (G,H) , brown], SALL4 [ (I,J) , brown], and CD44 [ (K,L) , brown] in subcutaneous venous malformation (SCVM) (A,C,E,G,I,K) and intramuscular venous malformation (IMVM) (B,D,F,H,J,L) . Endothelial staining of all six embryonic stem cell markers was present on the endothelium within both SCVM and IMVM samples. Nanog (A,B) , pSTAT3 (C,D) , SOX2 (G,H) , and CD44 (K,L) were also expressed on cells ( arrowheads ) away from the endothelium in both SCVM and IMVM samples. Nuclei were counterstained with hematoxylin (blue). Original magnification: 400×.

Figure Legend Snippet: 3,3′-Diaminobenzidine immunohistochemical-stained images demonstrating the expression of Nanog [ (A,B) , red], pSTAT3 [ (C,D) , brown], OCT4 [ (E,F) , brown], SOX2 [ (G,H) , brown], SALL4 [ (I,J) , brown], and CD44 [ (K,L) , brown] in subcutaneous venous malformation (SCVM) (A,C,E,G,I,K) and intramuscular venous malformation (IMVM) (B,D,F,H,J,L) . Endothelial staining of all six embryonic stem cell markers was present on the endothelium within both SCVM and IMVM samples. Nanog (A,B) , pSTAT3 (C,D) , SOX2 (G,H) , and CD44 (K,L) were also expressed on cells ( arrowheads ) away from the endothelium in both SCVM and IMVM samples. Nuclei were counterstained with hematoxylin (blue). Original magnification: 400×.

Techniques Used: Immunohistochemistry, Staining, Expressing

Representative hematoxylin and eosin stained subcutaneous venous malformation (SCVM) (A) and intramuscular venous malformation (IMVM) (B) sections demonstrating the characteristic ectatic venous channels. Representative sections of SCVM (C) and IMVM (D) showing minimal staining for D2-40 [ (C,D) , brown]. Nuclei were counterstained with hematoxylin [ (A–D) , blue]. Original magnifications: 400× (A,B) and 100× (C,D) .

Figure Legend Snippet: Representative hematoxylin and eosin stained subcutaneous venous malformation (SCVM) (A) and intramuscular venous malformation (IMVM) (B) sections demonstrating the characteristic ectatic venous channels. Representative sections of SCVM (C) and IMVM (D) showing minimal staining for D2-40 [ (C,D) , brown]. Nuclei were counterstained with hematoxylin [ (A–D) , blue]. Original magnifications: 400× (A,B) and 100× (C,D) .

Techniques Used: Staining

Representative immunofluorescent immunohistochemical-stained sections of subcutaneous venous malformation (SCVM) (A) and intramuscular venous malformation (IMVM) (B) samples, demonstrating the endothelium consisted of CD34 + (green)/ERG − (red) ( long arrows ), ERG + (red)/CD34 − (green) endothelium ( arrowheads ), and CD34 + (red)/ERG + (red) ( short arrows ) phenotypes. The CD34 + (green) endothelium expressed Nanog (red, arrows ) in SCVM (C) and IMVM (D) lesions with cells away from the endothelium also expressing Nanog (red, arrowheads ) within SCVM (C) and IMVM (D) lesions. The CD34 + (green) endothelium expressed pSTAT3 (red, arrows ) in both SCVM (E) and IMVM (F) lesions. Cells away from the endothelium also expressed pSTAT3 (red, arrowheads ) within SCVM (E) and IMVM (F) lesions. The ERG + (red) endothelium also expressed OCT4 (green, arrows ) in both SCVM (G) and IMVM (H) lesions. The CD34 + (green) endothelium expressed SOX2 (red, arrows ) in SCVM (I) and IMVM (J) lesions. Cells away from the endothelium also expressed SOX2 (red, arrowheads ) in SCVM (I) and IMVM (J) lesions. The ERG + endothelium (red) expressed SALL4 (green, arrows ) in SCVM (K) and IMVM (L) lesions. Dual staining of with SOX2 and SALL4 demonstrated the SALL4 + [ (M,N) , green] endothelial population expressed SOX2 [ (M,N) , red] in both SCVM (M) and IMVM (N) . The ERG + endothelium (red) expressed CD44 (green, arrows ) in SCVM (O) and IMVM (P) lesions with cells away from the endothelium also expressing CD44 (green, arrowheads ) in SCVM (O) and IMVM (P) . Cells outside of the endothelium in both SCVM (Q) and IMVM (R) co-expressed Nanog [ (Q,R) , red] and CD44 [ (Q,R) , green]. Cell nuclei were counterstained with 4′,6′-diamidino-2-phenylindole [ (A–R) , blue]. Scale bars: 20 µm.

Figure Legend Snippet: Representative immunofluorescent immunohistochemical-stained sections of subcutaneous venous malformation (SCVM) (A) and intramuscular venous malformation (IMVM) (B) samples, demonstrating the endothelium consisted of CD34 + (green)/ERG − (red) ( long arrows ), ERG + (red)/CD34 − (green) endothelium ( arrowheads ), and CD34 + (red)/ERG + (red) ( short arrows ) phenotypes. The CD34 + (green) endothelium expressed Nanog (red, arrows ) in SCVM (C) and IMVM (D) lesions with cells away from the endothelium also expressing Nanog (red, arrowheads ) within SCVM (C) and IMVM (D) lesions. The CD34 + (green) endothelium expressed pSTAT3 (red, arrows ) in both SCVM (E) and IMVM (F) lesions. Cells away from the endothelium also expressed pSTAT3 (red, arrowheads ) within SCVM (E) and IMVM (F) lesions. The ERG + (red) endothelium also expressed OCT4 (green, arrows ) in both SCVM (G) and IMVM (H) lesions. The CD34 + (green) endothelium expressed SOX2 (red, arrows ) in SCVM (I) and IMVM (J) lesions. Cells away from the endothelium also expressed SOX2 (red, arrowheads ) in SCVM (I) and IMVM (J) lesions. The ERG + endothelium (red) expressed SALL4 (green, arrows ) in SCVM (K) and IMVM (L) lesions. Dual staining of with SOX2 and SALL4 demonstrated the SALL4 + [ (M,N) , green] endothelial population expressed SOX2 [ (M,N) , red] in both SCVM (M) and IMVM (N) . The ERG + endothelium (red) expressed CD44 (green, arrows ) in SCVM (O) and IMVM (P) lesions with cells away from the endothelium also expressing CD44 (green, arrowheads ) in SCVM (O) and IMVM (P) . Cells outside of the endothelium in both SCVM (Q) and IMVM (R) co-expressed Nanog [ (Q,R) , red] and CD44 [ (Q,R) , green]. Cell nuclei were counterstained with 4′,6′-diamidino-2-phenylindole [ (A–R) , blue]. Scale bars: 20 µm.

Techniques Used: Immunohistochemistry, Staining, Expressing

Log 10 relative expression of OCT4, STAT3, and CD44 (A) and SOX2, Nanog, and SALL4 (B) mRNA transcripts in three subcutaneous venous malformation (SCVM) and three intramuscular venous malformation (IMVM) samples analyzed by NanoString (A) and RT-qPCR (B) analyses. Expression is depicted relative to the housekeeping gene GAPDH. OCT4 was detected in two SCVM and two IMVM samples (A) . STAT3 and CD44 (A) and SOX2 and SALL4 (B) were detected in all three samples. Nanog was detected in all three SCVM samples and two out of three IMVM samples (B) .

Figure Legend Snippet: Log 10 relative expression of OCT4, STAT3, and CD44 (A) and SOX2, Nanog, and SALL4 (B) mRNA transcripts in three subcutaneous venous malformation (SCVM) and three intramuscular venous malformation (IMVM) samples analyzed by NanoString (A) and RT-qPCR (B) analyses. Expression is depicted relative to the housekeeping gene GAPDH. OCT4 was detected in two SCVM and two IMVM samples (A) . STAT3 and CD44 (A) and SOX2 and SALL4 (B) were detected in all three samples. Nanog was detected in all three SCVM samples and two out of three IMVM samples (B) .

Techniques Used: Expressing, Quantitative RT-PCR

17) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

18) Product Images from "Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues"

Article Title: Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues

Journal:

doi: 10.2353/jmoldx.2008.070153

qRT-PCR analysis of RNA samples isolated with the RecoverAll or RNeasy kit. Total RNA was extracted in triplicate from five different FFPE tissue blocks using the indicated method. Each RNA sample was analyzed in duplicate using qRT-PCR assays specific

Figure Legend Snippet: qRT-PCR analysis of RNA samples isolated with the RecoverAll or RNeasy kit. Total RNA was extracted in triplicate from five different FFPE tissue blocks using the indicated method. Each RNA sample was analyzed in duplicate using qRT-PCR assays specific

Techniques Used: Quantitative RT-PCR, Isolation, Formalin-fixed Paraffin-Embedded

19) Product Images from "Transcriptomic Profiling of Human Peritumoral Neocortex Tissues Revealed Genes Possibly Involved in Tumor-Induced Epilepsy"

Article Title: Transcriptomic Profiling of Human Peritumoral Neocortex Tissues Revealed Genes Possibly Involved in Tumor-Induced Epilepsy

Journal: PLoS ONE

doi: 10.1371/journal.pone.0056077

Bioanalyzer profiles of FFPE human peritumoral tissue total RNA. The total RNA was extracted from FFPE peritumoral tissues using Qiagen RNA extraction kit for FFPE samples or using Qiagen RNeasy Mini kit for human peripheral blood mononuclear cells (PBMCs). The upper panel shows the Bioanalyzer results of two FFPE RNA samples and the lower panel shows the profiling of RNA freshly extracted from human PBMCs. The Bioanalyzer profiles were obtained using Agilent RNA Nano LabChip.

Figure Legend Snippet: Bioanalyzer profiles of FFPE human peritumoral tissue total RNA. The total RNA was extracted from FFPE peritumoral tissues using Qiagen RNA extraction kit for FFPE samples or using Qiagen RNeasy Mini kit for human peripheral blood mononuclear cells (PBMCs). The upper panel shows the Bioanalyzer results of two FFPE RNA samples and the lower panel shows the profiling of RNA freshly extracted from human PBMCs. The Bioanalyzer profiles were obtained using Agilent RNA Nano LabChip.

Techniques Used: Formalin-fixed Paraffin-Embedded, RNA Extraction

20) Product Images from "Transcriptomic Profiling of Human Peritumoral Neocortex Tissues Revealed Genes Possibly Involved in Tumor-Induced Epilepsy"

Article Title: Transcriptomic Profiling of Human Peritumoral Neocortex Tissues Revealed Genes Possibly Involved in Tumor-Induced Epilepsy

Journal: PLoS ONE

doi: 10.1371/journal.pone.0056077

Techniques Used: Formalin-fixed Paraffin-Embedded, RNA Extraction

21) Product Images from "Identification of a novel monocytic phenotype in Classic Hodgkin Lymphoma tumor microenvironment"

Article Title: Identification of a novel monocytic phenotype in Classic Hodgkin Lymphoma tumor microenvironment

Journal: PLoS ONE

doi: 10.1371/journal.pone.0224621

CD163, CD14 and SR-A expression in nodal CHL, lung and liver assessed by qRT-PCR. Total RNA was prepared from FFPE sections of nodal NSCHL (n = 2) and MCCHL (n = 2), from tissue (lung and liver), and differentiated THP-1 macrophages (positive control). After reverse transcription, qRT-PCR was used to quantify expression of CD68, CD163, and SR-A. Relative expression of CD163 and SR-A in macrophages was calculated by normalizing their Ct values to that of CD68 in the same sample (ΔCt), and then to their expression in THP-1 macrophages (ΔΔCt). CD163 expression was readily detected in nodal CHL and lung/liver (tissue), and to a lesser extent in NSCHL and MCCHL. SR-A expression was readily detected in tissue, but was only detected at very low levels in NSCHL and not detected (ND) in MCCHL.

Figure Legend Snippet: CD163, CD14 and SR-A expression in nodal CHL, lung and liver assessed by qRT-PCR. Total RNA was prepared from FFPE sections of nodal NSCHL (n = 2) and MCCHL (n = 2), from tissue (lung and liver), and differentiated THP-1 macrophages (positive control). After reverse transcription, qRT-PCR was used to quantify expression of CD68, CD163, and SR-A. Relative expression of CD163 and SR-A in macrophages was calculated by normalizing their Ct values to that of CD68 in the same sample (ΔCt), and then to their expression in THP-1 macrophages (ΔΔCt). CD163 expression was readily detected in nodal CHL and lung/liver (tissue), and to a lesser extent in NSCHL and MCCHL. SR-A expression was readily detected in tissue, but was only detected at very low levels in NSCHL and not detected (ND) in MCCHL.

Techniques Used: Expressing, Quantitative RT-PCR, Formalin-fixed Paraffin-Embedded, Positive Control

22) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

23) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

24) Product Images from "Spatial transcriptomics of tumor microenvironment in formalin-fixed paraffin-embedded breast cancer"

Article Title: Spatial transcriptomics of tumor microenvironment in formalin-fixed paraffin-embedded breast cancer

Journal: bioRxiv

doi: 10.1101/2020.01.31.928143

Assessment of RNA quantity and quality from microdissected TC and TIL. A. Original Qiagen RNeasy® FFPE Kit protocol . B-D. Yield, DV 200 and RIN of RNA extracted with different durations of tissue digestion with proteinase K. E. Modified protocol for RNA extraction from the original Qiagen RNeasy® FFPE Kit protocol. F. Yield of RNA collected from microdissected TC, TIL and fib from 7 samples of TNBC. G-I. RNA yield, RIN and DV 200 extracted from microdissected TIL and TC, according to the age of FFPE blocks. Dashed lines represent the minimal RNA quantity and quality required for subsequent RNA-sequencing. FFPE: formalin-fixed paraffin-embedded. RIN: RNA integrity number; DV200: percentage of RNA fragments > 200 nucleotides.

Figure Legend Snippet: Assessment of RNA quantity and quality from microdissected TC and TIL. A. Original Qiagen RNeasy® FFPE Kit protocol . B-D. Yield, DV 200 and RIN of RNA extracted with different durations of tissue digestion with proteinase K. E. Modified protocol for RNA extraction from the original Qiagen RNeasy® FFPE Kit protocol. F. Yield of RNA collected from microdissected TC, TIL and fib from 7 samples of TNBC. G-I. RNA yield, RIN and DV 200 extracted from microdissected TIL and TC, according to the age of FFPE blocks. Dashed lines represent the minimal RNA quantity and quality required for subsequent RNA-sequencing. FFPE: formalin-fixed paraffin-embedded. RIN: RNA integrity number; DV200: percentage of RNA fragments > 200 nucleotides.

Techniques Used: Formalin-fixed Paraffin-Embedded, Modification, RNA Extraction, RNA Sequencing Assay

25) Product Images from "Upregulation of P2Y2R, Active uPA, and PAI-1 Are Essential Components of Hantavirus Cardiopulmonary Syndrome"

Article Title: Upregulation of P2Y2R, Active uPA, and PAI-1 Are Essential Components of Hantavirus Cardiopulmonary Syndrome

Journal: Frontiers in Cellular and Infection Microbiology

doi: 10.3389/fcimb.2018.00169

Techniques Used: Expressing, Formalin-fixed Paraffin-Embedded, TaqMan Assay, Plasmid Preparation

26) Product Images from "Transcriptomic Profiling of Human Peritumoral Neocortex Tissues Revealed Genes Possibly Involved in Tumor-Induced Epilepsy"

Article Title: Transcriptomic Profiling of Human Peritumoral Neocortex Tissues Revealed Genes Possibly Involved in Tumor-Induced Epilepsy

Journal: PLoS ONE

doi: 10.1371/journal.pone.0056077

Techniques Used: Formalin-fixed Paraffin-Embedded, RNA Extraction

27) Product Images from "Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples"

Article Title: Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples

Journal: Scientific Reports

doi: 10.1038/srep21418

Effect of RNA purification method on RNA concentration and integrity. ( a ) RNA concentration of FFPE samples processed with Epicentre (E) or Qiagen (Q). Each boxplot represents 6 data points for NGP and HEK-293T FFPE cell pellets, and 20 data points for tumor FFPE samples. Statistical significance between Qiagen and Epicentre samples is calculated by 2-tailed paired t-test: (*)

Figure Legend Snippet: Effect of RNA purification method on RNA concentration and integrity. ( a ) RNA concentration of FFPE samples processed with Epicentre (E) or Qiagen (Q). Each boxplot represents 6 data points for NGP and HEK-293T FFPE cell pellets, and 20 data points for tumor FFPE samples. Statistical significance between Qiagen and Epicentre samples is calculated by 2-tailed paired t-test: (*)

Techniques Used: Purification, Concentration Assay, Formalin-fixed Paraffin-Embedded

Effect of gene-specific RT and whole transcriptome RT on RT-qPCR sensitivity. ( a ) Cq values for HEK-293T cell pellet FFPE samples processed with gene-specific RT or whole transcriptome RT. Each boxplot represents average Cq values from two RNA samples for 48 genes, shown for Epicentre RNA and Qiagen RNA isolates. Differences between gene-specific RT and whole transcriptome RT are significant (2-tailed paired t-test), (***)

Figure Legend Snippet: Effect of gene-specific RT and whole transcriptome RT on RT-qPCR sensitivity. ( a ) Cq values for HEK-293T cell pellet FFPE samples processed with gene-specific RT or whole transcriptome RT. Each boxplot represents average Cq values from two RNA samples for 48 genes, shown for Epicentre RNA and Qiagen RNA isolates. Differences between gene-specific RT and whole transcriptome RT are significant (2-tailed paired t-test), (***)

Techniques Used: Quantitative RT-PCR, Formalin-fixed Paraffin-Embedded

Overview of non-normalized gene expression (Cq values) in preamplified and non-preamplified samples processed with gene-specific RT and whole transcriptome RT. ( a ) Unsupervised hierarchical clustering of Cq values for 48 genes in 10 HEK-293T FFPE cell pellets and 8 no template controls (NTCs). Distance measure = Manhattan, clustering method = Ward. ( b ) Boxplot analysis for comparison of gene expression levels in preamplified samples (PA), non-preamplified gene-specific RT samples (GSP), non-preamplified whole transcriptome RT samples (WT) and no template controls (NTC), shown for Qiagen (Q) and Epicentre (E) RNA isolates. (*) All differences are significant (two-tailed paired t-test based, P

Figure Legend Snippet: Overview of non-normalized gene expression (Cq values) in preamplified and non-preamplified samples processed with gene-specific RT and whole transcriptome RT. ( a ) Unsupervised hierarchical clustering of Cq values for 48 genes in 10 HEK-293T FFPE cell pellets and 8 no template controls (NTCs). Distance measure = Manhattan, clustering method = Ward. ( b ) Boxplot analysis for comparison of gene expression levels in preamplified samples (PA), non-preamplified gene-specific RT samples (GSP), non-preamplified whole transcriptome RT samples (WT) and no template controls (NTC), shown for Qiagen (Q) and Epicentre (E) RNA isolates. (*) All differences are significant (two-tailed paired t-test based, P

Techniques Used: Expressing, Formalin-fixed Paraffin-Embedded, Two Tailed Test

28) Product Images from "Bromodomain Protein BRD4 Is a Transcriptional Repressor of Autophagy and Lysosomal Function"

Article Title: Bromodomain Protein BRD4 Is a Transcriptional Repressor of Autophagy and Lysosomal Function

Journal: Molecular Cell

doi: 10.1016/j.molcel.2017.04.027

Techniques Used: Expressing, Transfection, RNA Sequencing Assay, Quantitative RT-PCR

Techniques Used: Expressing, Transfection, Luciferase, Western Blot, Staining, Immunohistochemistry, Transgenic Assay, Mouse Assay, shRNA, Stable Transfection

29) Product Images from "CDK1 and CCNB1 as potential diagnostic markers of rhabdomyosarcoma: validation following bioinformatics analysis"

Article Title: CDK1 and CCNB1 as potential diagnostic markers of rhabdomyosarcoma: validation following bioinformatics analysis

Journal: BMC Medical Genomics

doi: 10.1186/s12920-019-0645-x

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Expressing

30) Product Images from "Noggin regulates foregut progenitor cell programming, and misexpression leads to esophageal atresia"

Article Title: Noggin regulates foregut progenitor cell programming, and misexpression leads to esophageal atresia

Journal: The Journal of Clinical Investigation

doi: 10.1172/JCI123597

NOG is selectively expressed in developing human esophagus but not in the trachea, and EA/TEF tissue lacks NOG. ( A ) Pathology samples from human autopsies stained for genes that have been previously known to be important in foregut development. Paraffin sections were used to perform IHC with NOG, BMP7, SHH (green), BMP4, BMP2, and SOX2 (red). All genes were present in both esophagus and trachea. However, NOG was missing from respiratory tissue. ( B ) Pathology samples from EA/TEF repair were collected to study NOG and BMP expression using IHC. On H E staining, a combination of esophageal and respiratory glands were found in atretic esophagus as well as in fistula. NOG is absent from EA/TEF samples when evaluated by IHC as well as RT-PCR ( B , D ). ( C ) Human esophageal and respiratory pathology samples stained for CK13 (red) and TFF3 (green). TEF from human neonate expresses both CK13 and TFF3. ( D ) RNA was isolated from paraffin samples of either esophagus of control neonates, or EA/TEF tissue obtained at the time of surgical repair. Positive control (+) is RNA extracted from Kato III cell line. *Pseudostratified columnar epithelium with cilia. Blue arrow indicates cilia. Black arrow indicates seromucinous glands. Inserts are ×2 magnification. Scale bars: 100 μm. C, control, T, TEF.

Figure Legend Snippet: NOG is selectively expressed in developing human esophagus but not in the trachea, and EA/TEF tissue lacks NOG. ( A ) Pathology samples from human autopsies stained for genes that have been previously known to be important in foregut development. Paraffin sections were used to perform IHC with NOG, BMP7, SHH (green), BMP4, BMP2, and SOX2 (red). All genes were present in both esophagus and trachea. However, NOG was missing from respiratory tissue. ( B ) Pathology samples from EA/TEF repair were collected to study NOG and BMP expression using IHC. On H E staining, a combination of esophageal and respiratory glands were found in atretic esophagus as well as in fistula. NOG is absent from EA/TEF samples when evaluated by IHC as well as RT-PCR ( B , D ). ( C ) Human esophageal and respiratory pathology samples stained for CK13 (red) and TFF3 (green). TEF from human neonate expresses both CK13 and TFF3. ( D ) RNA was isolated from paraffin samples of either esophagus of control neonates, or EA/TEF tissue obtained at the time of surgical repair. Positive control (+) is RNA extracted from Kato III cell line. *Pseudostratified columnar epithelium with cilia. Blue arrow indicates cilia. Black arrow indicates seromucinous glands. Inserts are ×2 magnification. Scale bars: 100 μm. C, control, T, TEF.

Techniques Used: Staining, Immunohistochemistry, Expressing, Reverse Transcription Polymerase Chain Reaction, Isolation, Positive Control

31) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

32) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

33) Product Images from "Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues"

Article Title: Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues

Journal:

doi: 10.2353/jmoldx.2008.070153

Techniques Used: Quantitative RT-PCR, Isolation, Formalin-fixed Paraffin-Embedded

34) Product Images from "Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?"

Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?

Journal: BMC Clinical Pathology

doi: 10.1186/s12907-016-0039-3

Techniques Used: Concentration Assay, Formalin-fixed Paraffin-Embedded, Isolation, Purification

35) Product Images from "Expression profiling with RNA from formalin-fixed, paraffin-embedded material"

Article Title: Expression profiling with RNA from formalin-fixed, paraffin-embedded material

Journal: BMC Medical Genomics

doi: 10.1186/1755-8794-1-9

Comparison of RNAs isolated according to different protocols . RNA was reverse transcribed in the presence of random primers (white boxes) or gene-specific primers (hatched boxes). Gene expression was measured from an equivalent of 4 ng of RNA by QPCR for five reference genes (GAPDH, GUSB, RPLP0, TFRC and UBB). Pearson correlations were computed between matched Cts for the five reference genes and each tumor RNA isolated from FF (A) and FFPE material. Shown are correlations between intact RNA and RNA isolated from FFPE material according to the RNeasy FFPE protocol (A versus B), intact RNA and RNA isolated from FFPE material according to the ncLysis system (A versus C) and intact RNA and RNA isolated according to our own protocol (A versus D).

Figure Legend Snippet: Comparison of RNAs isolated according to different protocols . RNA was reverse transcribed in the presence of random primers (white boxes) or gene-specific primers (hatched boxes). Gene expression was measured from an equivalent of 4 ng of RNA by QPCR for five reference genes (GAPDH, GUSB, RPLP0, TFRC and UBB). Pearson correlations were computed between matched Cts for the five reference genes and each tumor RNA isolated from FF (A) and FFPE material. Shown are correlations between intact RNA and RNA isolated from FFPE material according to the RNeasy FFPE protocol (A versus B), intact RNA and RNA isolated from FFPE material according to the ncLysis system (A versus C) and intact RNA and RNA isolated according to our own protocol (A versus D).

Techniques Used: Isolation, Expressing, Real-time Polymerase Chain Reaction, Formalin-fixed Paraffin-Embedded

Comparison of RNA isolation methods . Shown are the means of raw Cts of five reference genes (GAPDH, GUSB, RPLP0, TFRC, UBB) for intact RNA (◇, FF) and for RNA isolated from matched FFPE material according to the protocols of Qiagen (□, Q), Applied Biosystems (△, AB) and our own (○, own). Individual mean Cts of the 14 tumors and summarized box plots of Cts are shown in panel A and panel B, respectively. Tumors are aligned according to increasing Ct in FFPE-derived RNA (Qiagen protocol).

Figure Legend Snippet: Comparison of RNA isolation methods . Shown are the means of raw Cts of five reference genes (GAPDH, GUSB, RPLP0, TFRC, UBB) for intact RNA (◇, FF) and for RNA isolated from matched FFPE material according to the protocols of Qiagen (□, Q), Applied Biosystems (△, AB) and our own (○, own). Individual mean Cts of the 14 tumors and summarized box plots of Cts are shown in panel A and panel B, respectively. Tumors are aligned according to increasing Ct in FFPE-derived RNA (Qiagen protocol).

Techniques Used: Isolation, Formalin-fixed Paraffin-Embedded, Derivative Assay

RNA isolation and characterization . Total RNA was isolated from kryo-sections (lanes A) and from paraffin sections according to the RNeasy FFPE protocol of Qiagen (lanes B), the ncLysis protocol of Applied Biosystems (lanes C) or according to our own protocol (lanes D). Aliquots of each RNA were separated by capillary electrophoresis (Agilent Bioanalyzer) on Nano chips along with RNA ladder (L; Ambion). Shown are RNAs from two representative tumors (Tu#10 and #18).

Figure Legend Snippet: RNA isolation and characterization . Total RNA was isolated from kryo-sections (lanes A) and from paraffin sections according to the RNeasy FFPE protocol of Qiagen (lanes B), the ncLysis protocol of Applied Biosystems (lanes C) or according to our own protocol (lanes D). Aliquots of each RNA were separated by capillary electrophoresis (Agilent Bioanalyzer) on Nano chips along with RNA ladder (L; Ambion). Shown are RNAs from two representative tumors (Tu#10 and #18).

Techniques Used: Isolation, Formalin-fixed Paraffin-Embedded, Electrophoresis

36) Product Images from "Spatial transcriptomics of tumor microenvironment in formalin-fixed paraffin-embedded breast cancer"

Article Title: Spatial transcriptomics of tumor microenvironment in formalin-fixed paraffin-embedded breast cancer

Journal: bioRxiv

doi: 10.1101/2020.01.31.928143

Techniques Used: Formalin-fixed Paraffin-Embedded, Modification, RNA Extraction, RNA Sequencing Assay

37) Product Images from "A high-throughput method to detect RNA profiling by integration of RT-MLPA with next generation sequencing technology"

Article Title: A high-throughput method to detect RNA profiling by integration of RT-MLPA with next generation sequencing technology

Journal: Oncotarget

doi: 10.18632/oncotarget.17551

The RNA expression levels of 16 cancer-associated genes in patient #04 and #05 detected by both RT-MLPSeq and RT-qPCT methods The RNA levels of 16 genes, including Ki67, STK15, Survivin, CCNB1, MYBL2, GRB7, HER2, MMP11, CTSL2, ER, PGR, BCL2, SCUBE2, GSTM1, CD68, BAG1 in FFPE sections were normalized to the average Ct value of 5 reference genes (ACTB, GAPDH, RPLPO, GUSB, TFRC).

Figure Legend Snippet: The RNA expression levels of 16 cancer-associated genes in patient #04 and #05 detected by both RT-MLPSeq and RT-qPCT methods The RNA levels of 16 genes, including Ki67, STK15, Survivin, CCNB1, MYBL2, GRB7, HER2, MMP11, CTSL2, ER, PGR, BCL2, SCUBE2, GSTM1, CD68, BAG1 in FFPE sections were normalized to the average Ct value of 5 reference genes (ACTB, GAPDH, RPLPO, GUSB, TFRC).

Techniques Used: RNA Expression, Formalin-fixed Paraffin-Embedded

Recurrence scores of 11 breast cancer patients calculated by RT-qPCR and RT-MLPSeq methods RNA from FFPE sections of 11 breast cancer patients were extracted and reverse-transcribed into cDNA. Then cDNA from the same patients were separated to determine the relative expression levels of 21 gene by RT-qPCR and MLPSeq. Recurrence scores were finally calculated according to the algorithm presented by Paik et al.

Figure Legend Snippet: Recurrence scores of 11 breast cancer patients calculated by RT-qPCR and RT-MLPSeq methods RNA from FFPE sections of 11 breast cancer patients were extracted and reverse-transcribed into cDNA. Then cDNA from the same patients were separated to determine the relative expression levels of 21 gene by RT-qPCR and MLPSeq. Recurrence scores were finally calculated according to the algorithm presented by Paik et al.

Techniques Used: Quantitative RT-PCR, Formalin-fixed Paraffin-Embedded, Expressing

38) Product Images from "Phosphorylated TDP-43 (pTDP-43) aggregates in the axial skeletal muscle of patients with sporadic and familial amyotrophic lateral sclerosis"

Article Title: Phosphorylated TDP-43 (pTDP-43) aggregates in the axial skeletal muscle of patients with sporadic and familial amyotrophic lateral sclerosis

Journal: Acta Neuropathologica Communications

doi: 10.1186/s40478-018-0528-y

qPCR analysis was performed in 5 ALS muscle samples (“ALS1–5”) and 3 IBM muscle samples (“IBM1–3”), all containing p62 and pTDP-43 inclusions by immunohistochemical studies (see Results ). Three non-ALS, non-IBM samples with mild neurogenic atrophy in the muscle biopsy were also studied (“MSC1–3”). SQSTM1 and TARDBP were analyzed relative to the expression of two housekeeping genes ( 18 s , GAPDH ) and data shown are combined from two 96-well plates (4 replicates per sample and primer). There was a significant increase in relative normalized gene expression for both ALS and IBM samples ( a ), relative to controls (right) and this was most significant for SQSTM1 expression in ALS samples ( > 4-fold expression relative to controls, P

Figure Legend Snippet: qPCR analysis was performed in 5 ALS muscle samples (“ALS1–5”) and 3 IBM muscle samples (“IBM1–3”), all containing p62 and pTDP-43 inclusions by immunohistochemical studies (see Results ). Three non-ALS, non-IBM samples with mild neurogenic atrophy in the muscle biopsy were also studied (“MSC1–3”). SQSTM1 and TARDBP were analyzed relative to the expression of two housekeeping genes ( 18 s , GAPDH ) and data shown are combined from two 96-well plates (4 replicates per sample and primer). There was a significant increase in relative normalized gene expression for both ALS and IBM samples ( a ), relative to controls (right) and this was most significant for SQSTM1 expression in ALS samples ( > 4-fold expression relative to controls, P

Techniques Used: Real-time Polymerase Chain Reaction, Immunohistochemistry, Expressing

39) Product Images from "Fit for genomic and proteomic purposes: Sampling the fitness of nucleic acid and protein derivatives from formalin fixed paraffin embedded tissue"

Article Title: Fit for genomic and proteomic purposes: Sampling the fitness of nucleic acid and protein derivatives from formalin fixed paraffin embedded tissue

Journal: PLoS ONE

doi: 10.1371/journal.pone.0181756

Box and whiskers plots showing the distribution of absorbance ratios (A 260/280 ) for nucleic acids DNA, RNA, miRNA and for protein (A 280 ) from FFPE. Panel A shows derivatives from FFPE stored between 1990–2001 and Panel B derivative from FFPE stored between 2002–2013 stratified by storage duration (11 year intervals) and cancer tumor tissue type (adenocarcinoma, squamous cell, and papillary carcinoma).

Figure Legend Snippet: Box and whiskers plots showing the distribution of absorbance ratios (A 260/280 ) for nucleic acids DNA, RNA, miRNA and for protein (A 280 ) from FFPE. Panel A shows derivatives from FFPE stored between 1990–2001 and Panel B derivative from FFPE stored between 2002–2013 stratified by storage duration (11 year intervals) and cancer tumor tissue type (adenocarcinoma, squamous cell, and papillary carcinoma).

Techniques Used: Formalin-fixed Paraffin-Embedded

Fit for genomic and proteomic purposes by steps (numbered yellow boxes). In step 1, the ACCESS database of the ACSR at GWU was used to construct a sampling frame of available FFPE blocks by cancer case, which were the sampling units used to avoid selecting multiple FFPE blocks from the same individual. In step 2, the sampling frame of FFPE blocks was stratified by intervals of 11 years of storage (1990–2001 and 2002–2013, inclusive) and then the three tumor tissue types with the highest frequency of FFPE in the ACSR at GWU. Simple random sampling without replacement was conducted in each stratum until the targeted sample size of 20 FFPE blocks per storage duration and tumor tissue type was reached. In step 3 , commercial kits were employed to extract nucleic acids and protein from 10 μm FFPE sections from each block; a separate FFPE section was used for each type of nucleic acid or protein extraction. In step 4, an initial assessment for the presence of the nucleic acid or protein was conducted by ultraviolet absorbance (UV). In step 5, the purity and concentration of nucleic acid and protein extracts were determined by a SpectraDrop Micro-Volume Microplate with a SPECTRAmax 384PLUS plate reader and SoftMax Pro v6.4.1 software for device control and data analysis. In step 6, nucleic acid and protein derivatives were assigned to fitness categories as described in the Methods section. In step 7 , the fitness of each FFPE block was assessed by ranking the combined fitness of the derivatives as follows: FFPE blocks that met the “Fit Nucleic Acids and Proteins for Diverse Analyses” requirements included blocks in which all four derivatives (DNA, RNA, miRNA, and protein) were “Fit”. FFPE blocks that were categorized as “Fit Nucleic Acids for Diverse Genomic Analyses” included blocks that were determined to have “Fit” nucleic acid derivatives only. FFPE blocks that had one or two

Figure Legend Snippet: Fit for genomic and proteomic purposes by steps (numbered yellow boxes). In step 1, the ACCESS database of the ACSR at GWU was used to construct a sampling frame of available FFPE blocks by cancer case, which were the sampling units used to avoid selecting multiple FFPE blocks from the same individual. In step 2, the sampling frame of FFPE blocks was stratified by intervals of 11 years of storage (1990–2001 and 2002–2013, inclusive) and then the three tumor tissue types with the highest frequency of FFPE in the ACSR at GWU. Simple random sampling without replacement was conducted in each stratum until the targeted sample size of 20 FFPE blocks per storage duration and tumor tissue type was reached. In step 3 , commercial kits were employed to extract nucleic acids and protein from 10 μm FFPE sections from each block; a separate FFPE section was used for each type of nucleic acid or protein extraction. In step 4, an initial assessment for the presence of the nucleic acid or protein was conducted by ultraviolet absorbance (UV). In step 5, the purity and concentration of nucleic acid and protein extracts were determined by a SpectraDrop Micro-Volume Microplate with a SPECTRAmax 384PLUS plate reader and SoftMax Pro v6.4.1 software for device control and data analysis. In step 6, nucleic acid and protein derivatives were assigned to fitness categories as described in the Methods section. In step 7 , the fitness of each FFPE block was assessed by ranking the combined fitness of the derivatives as follows: FFPE blocks that met the “Fit Nucleic Acids and Proteins for Diverse Analyses” requirements included blocks in which all four derivatives (DNA, RNA, miRNA, and protein) were “Fit”. FFPE blocks that were categorized as “Fit Nucleic Acids for Diverse Genomic Analyses” included blocks that were determined to have “Fit” nucleic acid derivatives only. FFPE blocks that had one or two "fit" or "above fit" derivative out of the three nucleic acid derivatives and “unfit”, "fit" or "above fit" protein derivatives, were considered “Fit for a Specific Genomic or Proteomic Analysis”. In step 8, if an FFPE block had no “Fit” molecular derivatives, it was considered a “Bad Block”.

Techniques Used: Construct, Sampling, Formalin-fixed Paraffin-Embedded, Blocking Assay, Protein Extraction, Concentration Assay, Software

Box and whiskers plots showing the distribution of concentration (nanograms per microliter) for the nucleic acids DNA, RNA, and miRNA co-extracted from FFPE. Panel A shows derivatives from FFPE stored between 1990–2001 and Panel B shows derivative from FFPE stored between 2002–2013.

Figure Legend Snippet: Box and whiskers plots showing the distribution of concentration (nanograms per microliter) for the nucleic acids DNA, RNA, and miRNA co-extracted from FFPE. Panel A shows derivatives from FFPE stored between 1990–2001 and Panel B shows derivative from FFPE stored between 2002–2013.

Techniques Used: Concentration Assay, Formalin-fixed Paraffin-Embedded

40) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Journal: BMC Medical Research Methodology

doi: 10.1186/s12874-018-0628-1

Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

DNA Extraction:

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
Article Snippet: .. The macro-dissected tumor area from one tissue section was used for RNA isolation using the RNeasy® FFPE kit (Qiagen, Hilden, Germany) and the tumor area from the second section was used for DNA isolation using the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), following the manufacturers’ instructions. .. Quantity and quality measurements The quantity and purity (A260/A280) of the extracted DNA and RNA was measured using the NanoDrop ND-2000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA).

Isolation:

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
Article Snippet: .. Assessment of nucleic acids extraction kits from FFPE biopsies with normal histology The study material, consisting of 30 FFPE prostate biopsies with normal histology, was randomly divided into three different groups; 1) ten biopsies for comparison between the High Pure FFPE RNA Micro Kit (Roche Diagnostics, West Sussex, UK) and the RNeasy® FFPE kit (Qiagen, Hilden, Germany), 2) ten biopsies for comparison between the High Pure DNA FFPET Isolation Kit (Roche Diagnostics, West Sussex, UK) and the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), and 3) ten biopsies for comparison of the best performing DNA and RNA kits from the two previous steps to the AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany). .. In order to minimize the risk of variation due to different operators, the same operator performed all extractions with one kit (e.g. all extractions using the RNeasy® FFPE kit).

Formalin-fixed Paraffin-Embedded:

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
Article Snippet: .. Based on the results from the assessment of nucleic acid extraction kits, DNA and RNA were extracted from two serial sections of the biopsies using the QIAamp® DNA FFPE Tissue Kit and RNeasy® FFPE kit. ..

Article Title: Upregulation of P2Y2R, Active uPA, and PAI-1 Are Essential Components of Hantavirus Cardiopulmonary Syndrome
Article Snippet: .. To measure the P2Y2 R expression levels in the tissue segments, RNA was extracted from 10 μm sections of the FFPE blocks using the Qiagen RNeasy FFPE kit (cat# 73504) and the instructions therein. .. The extracted RNA was quantified with a Thermo Fisher Scientific Nanodrop spectrophotometer.

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
Article Snippet: .. Figure a-c shows a comparison of RNA yields, purity (A260/A280) and RIN-values obtained from samples extracted with the High Pure FFPE RNA Micro kit and the RNeasy® FFPE kit, respectively. ..

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
Article Snippet: .. The RNeasy® FFPE kit resulted in consistently higher RNA yields (mean yield 16.3 ng/μl) ranging from 8.1 ng/μl to 20.8 ng/μl compared to the samples extracted with High Pure FFPE kit (mean yield 5.6 ng/μl) ranging from 2.2 ng/μl to 11.2 ng/μl (p < 0.001). .. Furthermore, both the A260/A280 ratios and RIN-values in samples extracted with the RNeasy® FFPE kit were higher (mean A260/A280 = 1.55, mean RIN-value = 1.98) compared to samples extracted with the High Pure kit (mean A260/A80 = 1.38, mean RIN-value = 1.04) (p = 0.03 and p < 0.001, respectively).

Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
Article Snippet: .. In order to minimize the risk of variation due to different operators, the same operator performed all extractions with one kit (e.g. all extractions using the RNeasy® FFPE kit). .. In the comparison between a) the High Pure FFPE RNA Micro kit and the RNeasy® FFPE kit and b) the High Pure FFPET DNA Isolation kit to the QIAamp® DNA FFPE Tissue kit, three serial sections of 10 μm were cut from ten biopsies with normal histology.

Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
Article Snippet: .. The RNeasy FFPE kit gave extraction efficiencies of 86% when processing up to 20 μm of tissue, above this the efficiencies were much less. .. We felt these small losses in yield (~14%) were an acceptable compromise for the increase in concentration achieved through combining tissue sections (Fig. ).

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