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Illumina Inc rnaseq
Expression pattern <t>of</t> <t>TYK2</t> , a T1D candidate gene, during human pancreatic development. a Schematic representation of the pancreatic differentiation protocol. The figure was partly generated using Servier Medical Art. b Heatmap of pancreatic lineage genes from deep <t>RNAseq</t> analysis at Stage (S) 1 (definitive endoderm), S4 (pancreatic-progenitors), and S7 (SC-islets). c Similar heatmap for known T1D candidate genes. Each gene is shown with a multiple testing corrected p value generated for the longitudinal differential expression of the gene during differentiation ( n = 5). d Relative expression of TYK2 during pancreatic differentiation shown by qRT-PCR ( n = 6) and e by immunoblot analysis for TYK2 protein. Tubulin was used as a loading control ( n = 3). f Expression pattern of TYK2 in human fetal pancreas samples at 40 to 70 days post conception ( n = 16). For d and f , significance was determined using one-way ANOVA with Tukey’s multiple comparison test, box and whiskers plots showing the median with whiskers extending from minimum to maximum values. * p
Rnaseq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 86 stars, based on 40 article reviews
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1) Product Images from "The type 1 diabetes gene TYK2 regulates β-cell development and its responses to interferon-α"

Article Title: The type 1 diabetes gene TYK2 regulates β-cell development and its responses to interferon-α

Journal: Nature Communications

doi: 10.1038/s41467-022-34069-z

Expression pattern of TYK2 , a T1D candidate gene, during human pancreatic development. a Schematic representation of the pancreatic differentiation protocol. The figure was partly generated using Servier Medical Art. b Heatmap of pancreatic lineage genes from deep RNAseq analysis at Stage (S) 1 (definitive endoderm), S4 (pancreatic-progenitors), and S7 (SC-islets). c Similar heatmap for known T1D candidate genes. Each gene is shown with a multiple testing corrected p value generated for the longitudinal differential expression of the gene during differentiation ( n = 5). d Relative expression of TYK2 during pancreatic differentiation shown by qRT-PCR ( n = 6) and e by immunoblot analysis for TYK2 protein. Tubulin was used as a loading control ( n = 3). f Expression pattern of TYK2 in human fetal pancreas samples at 40 to 70 days post conception ( n = 16). For d and f , significance was determined using one-way ANOVA with Tukey’s multiple comparison test, box and whiskers plots showing the median with whiskers extending from minimum to maximum values. * p
Figure Legend Snippet: Expression pattern of TYK2 , a T1D candidate gene, during human pancreatic development. a Schematic representation of the pancreatic differentiation protocol. The figure was partly generated using Servier Medical Art. b Heatmap of pancreatic lineage genes from deep RNAseq analysis at Stage (S) 1 (definitive endoderm), S4 (pancreatic-progenitors), and S7 (SC-islets). c Similar heatmap for known T1D candidate genes. Each gene is shown with a multiple testing corrected p value generated for the longitudinal differential expression of the gene during differentiation ( n = 5). d Relative expression of TYK2 during pancreatic differentiation shown by qRT-PCR ( n = 6) and e by immunoblot analysis for TYK2 protein. Tubulin was used as a loading control ( n = 3). f Expression pattern of TYK2 in human fetal pancreas samples at 40 to 70 days post conception ( n = 16). For d and f , significance was determined using one-way ANOVA with Tukey’s multiple comparison test, box and whiskers plots showing the median with whiskers extending from minimum to maximum values. * p

Techniques Used: Expressing, Generated, Quantitative RT-PCR

TYK2 negatively regulates KRAS expression. a Schematic for bulk RNAseq experiments for WT and TYK2 KO cells ( n = 3). The figure was generated using Servier Medical Art. b Principal component (PC) analysis of the bulk RNA-seq samples. Filled circles, WT cells; empty circles, KO cells. p -value (linear regression comparison) PC1~genotype of Stage (S) 5 is indicated. c Volcano plot for S5 differentially expressed genes for WT and KO. Significantly downregulated genes, iris blue; upregulated genes, soft red. Selected genes of interest are highlighted. d , e FPKM values for NEUROG3 and NKX2-2 expression at different differentiation stages. p -value (DESeq2) is indicated for S5. f Selected up- and down- regulated Reactome enrichment pathways in S5 KO cells compared to WT. g FPKM values for KRAS expression. h Relative transcript levels of KRAS with qRT-PCR in hiPSCs, S4 and S5 cells. i Immunoblot for KRAS at S4 and S5. Normalization with tubulin densitometric values are indicated in the panel ( n = 3). j Immunoblot for KRAS at S4 in WT and KO cells following TYK2i treatment during S3–S4. k Densitometric analysis of panel j ( n = 3). l Correlation of TYK2 and NEUROG3 expression in human fetal pancreas ( n = 16). Pearson’s correlation after log normalization of counts. m Correlation of KRAS and TYK2 expression; and n KRAS and INS expression in human islets ( n = 191). Pearson’s correlations r and significance levels p are indicated in the panels. o Schematic of TYK2 overexpression experiments. p Immunoblot for TYK2 48 h post pCMV-TYK2 electroporation during S5. β-actin used as a loading control ( n = 2). qRT-PCR relative transcript levels 24 h post pCMV-TYK2 overexpression during S5 for q TYK2 , r KRAS , and s NEUROG3 ( n = 3). Two-tailed unpaired t -tests were applied. * p
Figure Legend Snippet: TYK2 negatively regulates KRAS expression. a Schematic for bulk RNAseq experiments for WT and TYK2 KO cells ( n = 3). The figure was generated using Servier Medical Art. b Principal component (PC) analysis of the bulk RNA-seq samples. Filled circles, WT cells; empty circles, KO cells. p -value (linear regression comparison) PC1~genotype of Stage (S) 5 is indicated. c Volcano plot for S5 differentially expressed genes for WT and KO. Significantly downregulated genes, iris blue; upregulated genes, soft red. Selected genes of interest are highlighted. d , e FPKM values for NEUROG3 and NKX2-2 expression at different differentiation stages. p -value (DESeq2) is indicated for S5. f Selected up- and down- regulated Reactome enrichment pathways in S5 KO cells compared to WT. g FPKM values for KRAS expression. h Relative transcript levels of KRAS with qRT-PCR in hiPSCs, S4 and S5 cells. i Immunoblot for KRAS at S4 and S5. Normalization with tubulin densitometric values are indicated in the panel ( n = 3). j Immunoblot for KRAS at S4 in WT and KO cells following TYK2i treatment during S3–S4. k Densitometric analysis of panel j ( n = 3). l Correlation of TYK2 and NEUROG3 expression in human fetal pancreas ( n = 16). Pearson’s correlation after log normalization of counts. m Correlation of KRAS and TYK2 expression; and n KRAS and INS expression in human islets ( n = 191). Pearson’s correlations r and significance levels p are indicated in the panels. o Schematic of TYK2 overexpression experiments. p Immunoblot for TYK2 48 h post pCMV-TYK2 electroporation during S5. β-actin used as a loading control ( n = 2). qRT-PCR relative transcript levels 24 h post pCMV-TYK2 overexpression during S5 for q TYK2 , r KRAS , and s NEUROG3 ( n = 3). Two-tailed unpaired t -tests were applied. * p

Techniques Used: Expressing, Generated, RNA Sequencing Assay, Quantitative RT-PCR, Over Expression, Electroporation, Two Tailed Test

2) Product Images from "A rapid alkalinization factor-like peptide EaF82 impairs tapetum degeneration during pollen development"

Article Title: A rapid alkalinization factor-like peptide EaF82 impairs tapetum degeneration during pollen development

Journal: bioRxiv

doi: 10.1101/2022.08.11.503650

The functional characterization and RNAseq analysis of Arabidopsis transgenic 35Sp::EaF82 lines (TC-1 and -2) compared to wild-type (WT) and vector control (C). a RT-PCR of leaf tissues using primer pair specific to EaF82 and 18S rRNA . +: plasmid DNA. b Immunoblot of leaf proteins against anti-EaF82. Stained blot shows protein loading. M: protein size marker. c Normal growth of TC and WT plants. d Aborted siliques in TC-1 and TC-2. e Immunoblot of proteins from unopened whole flowers against anti-EaF82. f Stained pollen and g germinated pollen. The descriptions are the same as in Fig. 2 . Bar=100 μm. h Histogram of the silique lengths. Data plotted are the percentages of total siliques. n: numbers of siliques. i The number of up- and down-regulated DEGs (≥ 2-fold) in TC-1 and -2 lines. j Enriched GO terms from down-regulated DEGs related to pH regulation and cell wall modification.
Figure Legend Snippet: The functional characterization and RNAseq analysis of Arabidopsis transgenic 35Sp::EaF82 lines (TC-1 and -2) compared to wild-type (WT) and vector control (C). a RT-PCR of leaf tissues using primer pair specific to EaF82 and 18S rRNA . +: plasmid DNA. b Immunoblot of leaf proteins against anti-EaF82. Stained blot shows protein loading. M: protein size marker. c Normal growth of TC and WT plants. d Aborted siliques in TC-1 and TC-2. e Immunoblot of proteins from unopened whole flowers against anti-EaF82. f Stained pollen and g germinated pollen. The descriptions are the same as in Fig. 2 . Bar=100 μm. h Histogram of the silique lengths. Data plotted are the percentages of total siliques. n: numbers of siliques. i The number of up- and down-regulated DEGs (≥ 2-fold) in TC-1 and -2 lines. j Enriched GO terms from down-regulated DEGs related to pH regulation and cell wall modification.

Techniques Used: Functional Assay, Transgenic Assay, Plasmid Preparation, Reverse Transcription Polymerase Chain Reaction, Staining, Marker, Modification

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