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Sample GSM1180111 Query DataSets for GSM1180111
Status Public on Jul 04, 2013
Title mouse/in vitro activated B cell/H3K36me2/rep2
Sample type SRA
Source name mouse, in vitro activated B cells
Organism Mus musculus
Characteristics antibody: H3K36me2
cell type: in vitro activated B cells
strain: C57BL/6
Growth protocol CD43− B cells were isolated from spleens by immunomagnetic depletion (Miltenyi Biotech). Purified cells were then activated in RPMI-1640 media with 10% (vol/vol) FCS, 1×antibiotic-antimycotic, 1% (wt/vol) glutamine, 1× non-essential amino acids, 1% (wt/vol) sodium pyruvate, 53uM 2-beta-mercapto-ethanol, and 10 mM Hepes for 72 h in the presence of 50ug/mL of LPS (Escherichia coli 0111:B4; Sigma) and 2.5 ng/mL of IL-4 (Sigma).
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H3K36me2 antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Image analysis, base calling, quality filtering: Standard settings of GAPipeline using PhiX control; ***Raw data***: Fastq files contain full length reads that passed the chastity filter. Qualities were scaled to phred33 format for all files. ***Wig file***: Reads were aligned to the mouse genome (build mm9) with bowtie accepting only reads that had a unique match in the genome in their top quality stratum (bowtie 0.12.8, --best --all --strata -m1 -n2 -l50). Redundancy was capped at a maximum of 3 identically aligned reads, and reads shifted by half the approximate fragment size of 120 towards the fragment center were counted in 100 nt bins along the genome. Counts were normalized to the non redundant library size and bin size such that the final units are reads per kb per million (RPKM).
Submission date Jul 03, 2013
Last update date May 15, 2019
Contact name Seolkyoung Jung
Organization name NIH
Department NIAMS
Lab biodata mining and discovery section
Street address 10 Center Dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL13112
Series (1)
GSE48514 A mouse model of endemic Burkitt translocations reveals the long-range boundaries of Ig-mediated oncogene deregulation
BioSample SAMN02225383
SRA SRX317634

Supplementary file Size Download File type/resource
GSM1180111_r120328A_l3i4_aB_wt_H3K36me2.wig.gz 30.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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