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Fig. 1 | Genome Medicine

Fig. 1

From: Nuclear Wiskott–Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells

Fig. 1

ChIP-seq analysis of WASp enriched genes. a The F-8 anti-WASp Ab specifically recognizes WASp in total thymocyte lysates, nuclear extracts (NE), and cytosolic extracts (CE). Heavy chain of mouse IgG (IgGhc) is observed in eluted IP samples. GAPDH was used as a sample loading control for total lysates. b WASp is abundant in NE of WT thymocyte when compared to NE of WT spleen CD4+ T cells. Heavy chain of mouse IgG (IgGhc) is observed in eluted IP samples. GAPDH was used as a sample loading control for total lysates. These data are representative of four (thymus fractionation) and two (spleen CD4+ T cell fractionation) independent biological replicates. c ChIP-seq analysis of thymocytes and spleen CD4+ T cells flowchart. WASp-enriched genes by ChIP-seq analysis of WT thymocytes performed under high stringency condition. WASp-enriched genes by ChIP-seq analysis of spleen CD4+ T cells performed under low stringency conditions and compared to a ChIP-seq dataset from control Ab-free spleen CD4+ T cells. All common genes were subtracted from the spleen CD4+ T cells dataset. Both ChIP-seq datasets were then aligned and compared to identify common genes in thymocytes and spleen CD4+ T cells. d Distribution of distance from WASp ChIP-seq gene peaks to the nearest transcription start site (TSS) defined according to the positions of RefSeq TSSs using the CHIPseek software. Negative values indicate 5’ of the TSS, positive values indicate 3’ of the TSS. e Annotation of WASp ChIP-seq gene peak positions within intergenic and genic regions using CHIPseek software. By default promoter-TSS annotation defined as area from – 1 kb to + 100 bp of the TSS position and transcription termination site area (TTS) defined from – 100 bp to + 1 kb of the TTS position. f Functional groups of peak-corresponding genes in WASp ChIP-seq refined datasets. Additional file 1: Figure S1–S3 and Additional file 3: sheets 1 and 2

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