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Sample GSM2827790 Query DataSets for GSM2827790
Status Public on May 31, 2018
Title B cells 1
Sample type SRA
Source name B cells
Organism Homo sapiens
Characteristics subject: 1
tissue: Peripheral blood
cell type: B lymphocytes
Extracted molecule genomic DNA
Extraction protocol In situ HiC was performed as described by Rao et al (Cell 2014; PMID: 25497547).
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing Reads pairs from each sample were aligned to the human genome and counted into 50 kB bin pairs using the R package diffHic v1.6.0.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.
Submission date Oct 23, 2017
Last update date May 15, 2019
Contact name Gordon K Smyth
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
Platform ID GPL18573
Series (2)
GSE105776 In situ Hi-C profiles of human CD4+ T cells, CD8+ T cells and B cells
GSE126117 RNA-seq, ATAC-seq and Hi-C profiles of B cells and naïve and activated T cells from human peripheral blood
BioSample SAMN07822217
SRA SRX3312500

Supplementary file Size Download File type/resource
GSM2827790_HB1_hg_t.mtx.gz 302.0 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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