Cancer Genomics, ICR, cell line data

Richard R Houlston
richard.houlston@icr.ac.uk

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Dataset ID	Description	Technology	Samples
EGAD50000000294	Ultra high-resolution chromatin capture data in CACO2, CL11, HT29, SW403, SW480, SW948 MSS CRC cell lines	Illumina NovaSeq 6000	6
EGAD50000000295	ChIP-Seq data for CTCF, H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me3 in C32, CL11, HT29, SW403, SW480, SW948 MSS CRC cell lines	Illumina NovaSeq 6000	6
EGAD50000000296	ATAC-Seq data for C32, CACO2, CL11, HT29, SW403, SW480, SW948 MSS CRC cell lines, and HCEC-1CT normal colon cell line	Illumina NovaSeq 6000	8
EGAD50000000297	RNA-Seq data for C32, CACO2, CL11, HT29, SW403, SW948 MSS CRC cell lines and HCEC-1CT normal colon cell line	Illumina NovaSeq 6000	7
EGAD50000000375	We performed a systematic, genome-wide investigation of enhancer regions in colorectal cancer (CRC). We identified 12,117 putative enhancer regions using H3K27ac and H3Kme1 ChIP-seq and ATAC-seq. We performed scRNA-seq in HT29 and SW480 (MSS CRC cell lines) using the Parse Biosciences WT-mega kit with CRISPRi/dCas9 inhibition of these regions (Perturb-seq). The Parse split-pipe pipeline was used to demultiplex the raw fastq files into the processed files (mtx files for genes and gRNA) for each cell line.	Illumina NovaSeq 6000	2
EGAD50000000596	Massively Parallel Reporter Assays (MPRA) of colorectal cell lines HCEC-1CT (normal colon) and HT29 and SW403 (MSS cancer). Probes identified using the CRC GWAS.	Illumina NovaSeq 6000	3