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Sample GSM3734879 Query DataSets for GSM3734879
Status Public on Sep 25, 2019
Title Splenic_nonsti_NIPBL_2
Sample type SRA
 
Source name Splenic mature B cells
Organism Mus musculus
Characteristics cell type: AID-deficient Splenic mature B cells
passages: 0 (primary mature splenic B cells)
strain: C57BL/6
chip antibody: NIPBL (Bethyl, A301-779A)
treatment: without stimulation
Treatment protocol Purified B cells were stimulated with either aCD40/IL4 for 48 hrs; CH12F3 cell lines were cultured in lymphocyte medium R15 and stimulated with anti-CD40+IL4+TGF-β for 24 hrs.
Growth protocol RPMI1640+10% FBS
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (IP-202-1012).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 550
 
Data processing Reads were aligned using bowtie2 with --non-deterministic flag
peaks were called with MACS2 with the following flags: --nomodel --keep-dup all --extsize 51 --nolambda -B --SPMR
wig files were generated using USCS utilities bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated for displaying
 
Submission date Apr 24, 2019
Last update date Sep 26, 2019
Contact name Frederick W Alt
E-mail(s) jianqiao.hu@childrens.harvard.edu
Organization name Boston Children's Hospital
Department PCMM
Lab Alt
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL21626
Series (2)
GSE130264 Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching [ChIP-Seq]
GSE130270 Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching
Relations
BioSample SAMN11491205
SRA SRX5730168

Supplementary file Size Download File type/resource
GSM3734879_Splenic_nonsti_NIPBL_2.broadPeak.gz 17.9 Mb (ftp)(http) BROADPEAK
GSM3734879_Splenic_nonsti_NIPBL_2.bw 63.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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