|
| 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 |
