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Sample GSM4431516 Query DataSets for GSM4431516
Status Public on Dec 08, 2020
Title B cell activation 33 hours 1
Sample type SRA
 
Source name Activated B cells
Organism Mus musculus
Characteristics strain: C57BL/6
activation time after lps stimulation: 33 hours (imminent division)
Treatment protocol Naïve B cells were negatively isolated (Miltenyi, 130-090-862), CTV labelled and stimulated with 25μg/ml LPS (Salmonella typhosa origin, Sigma)
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with formaldehyde as described by Rao et al (Cell 2014; PMID: 25497547)
In situ Hi-C 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 mouse genome and counted into 50 kB bin pairs using the R package diffHic v1.9.1.
Genome_build: mm10
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 Mar 24, 2020
Last update date Dec 08, 2020
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
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 GPL19057
Series (2)
GSE147467 In situ HiC of primary mouse B cell progenitor populations after activation with LPS
GSE147497 RNA-seq and in situ Hi-C of primary mouse B cell progenitor populations after activation with LPS
Relations
BioSample SAMN14441445
SRA SRX7983465

Supplementary file Size Download File type/resource
GSM4431516_B33_1.mtx.gz 216.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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