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Sample GSM2225739 Query DataSets for GSM2225739
Status Public on Sep 26, 2016
Title HiC_NB_rep_1
Sample type SRA
 
Source name purified human naïve B cells
Organism Homo sapiens
Characteristics subject status: healthy individual
tissue: tonsils
cell type: purified human naive B cells
cell subtype: IgD+ CD38low
Extracted molecule genomic DNA
Extraction protocol Primary human mature naïve B-cells (IgD+CD38lo; NB) and GCB-cells (CD77+CD38hi; GCB) were purified from tonsils of healthy individuals.
Hi-C DNA templates were generated as previously described (Lieberman-Aiden et al., 2009). RNA-seq libraries were prepared using the Illumina TruSeq RNA sample kits according to the manufacturer.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description HiC in naïve B cells replicate 1
processed data file: hic_NB_intra.bed.txt.gz, hic_NB_inter.sif.gz
Data processing HiC: We aligned the two ends of the paired reads separately to the reference human genome hg18 using the BWA aligner. Reads mapped ambiguously to multiple locations on the genome were discarded. We further used an in-house pipeline and filtered out clonal reads caused by PCR artifacts based on the 5’ and 3’ read positions, removed non-ligated DNA fragments, and retained interactions with consistent expected placement relative to HindIII enzyme digestion sites.
RNA-seq: We aligned the paired-end RNA-seq reads to the RefSeq transcripts using Tophat, removed clonal reads caused by PCR artifacts, and quantified expression levels in RPKM (reads per kilobase of exon model per million mapped reads) units using an in-house program.
Genome_build: hg18
Supplementary_files_format_and_content: RPKM: tab delimited file containing the RPKM for each gene/transcript.
Supplementary_files_format_and_content: BED.TXT: intra-chromosomal interactions in UCSC BED format (to store the interactions' chromosome and start and end positions). Interactions are merged from all replicates.
Supplementary_files_format_and_content: SIF: inter-chromosomal interactions; each row consists of the start and end coordinates of each paired-end read. Interactions are merged from all replicates.
 
Submission date Jul 05, 2016
Last update date May 15, 2019
Contact name David Soong
Organization name Weill Cornell Medical College
Street address 1305 York Avenue
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL11154
Series (1)
GSE84022 BCL6-centric reorganization of the genome during B cell affinity maturation
Relations
BioSample SAMN05359748
SRA SRX1897606

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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