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Sample GSM4957607 Query DataSets for GSM4957607
Status Public on Sep 30, 2021
Title RING1B_ChIPSeq rep 2
Sample type SRA
Source name resting B cells isolated from spleen
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: WT
cell type: Resting B cells
chip antibody: RING1B (MBL - D139-3)
Extracted molecule genomic DNA
Extraction protocol Spleens were isolated from 6- to 10-week-old C57B6 mice and homogenized through a sieve in B cell culture medium (RPMI-1640 (Lonza), 10% fetal calf serum (FCS) (Sigma), 0.1 U/ml penicillin (Lonza), 0.1 μg/ml streptomycin (Lonza), 2mM L-Glutamine (Lonza), 50μM beta-mercaptoethanol (Gibco)). The cell suspension was centrifuged on a Ficoll-Paque (GE Healthcare) cushion and the buffy coat layer was resuspended at a concentration of 1x 10e8 cells/ml in PBS + 2% FCS/ 1mM EDTA. Resting B cells were isolated using an EasySep Negative Selection- Mouse B Cell Isolation Kit (STEMCELL Technologies), which depletes for non-B cell markers and activated CD43+ B cells.
5ng of ChIP/Input DNA was used to prepare libraries using the NEBNext® Ultra™ II DNA LibraryPrep Kit for Illumina following the manufacturer recommendations. Library quality and quantity were assessed on a Bioanalyser and Qubit, respectively. Libraries were sequenced on an Illumina Hiseq 2500 (v4 chemistry), and single-end 50bp reads or paired-end 100bp reads per sample were generated.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description Ring1B PS2
Three biological replicates Ring1B PS1, Ring1B PS2 and Ring1B PS3 were merged for downstream analysis. More details please see the Data processing section.
Data processing Illumina CASAVA 1.8.4 software used for basecalling.
Raw reads were aligned to UCSC mm9 mouse genome obtained from iGenome with BWA (0.7.5a) for single-end reads and bowtie2 (2.3.4) with arguments -p 8 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 for paired-end reads.
Aligned reads were sorted and converted to bam by samtools (1.6).
Duplicated reads were removed by Picard MarkDuplicates tool (1.9).
Merged bam files from biological replicates were produced by samtools.
Duplicated reads were removed from merged bam files by Picard MarkDuplicates tool (1.9).
bigWig files were generated from merged duplicated reads removed bam files by bedtools genomeCoverageBed (normalized to Reads Per Million; RPM) and bedGraphToBigWig obtained from UCSC.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig files
Submission date Dec 04, 2020
Last update date Sep 30, 2021
Contact name LMS Bioinformatics Core
Organization name MRC London Institute of Medical Sciences
Department Bioinformatics Core
Street address Hammersmith Hospital Campus, Du Cane Road
City London
ZIP/Postal code W12 0NN
Country United Kingdom
Platform ID GPL17021
Series (2)
GSE162703 Genome-wide maps of transcription factor binding and histone modifications in splenic resting B cells isolated from mice
GSE162704 RUNX1 controls the rate of cell cycle entry during naive B cell activation by regulating expression of cell cycle and immunomodulatory genes in response to BCR stimulation
BioSample SAMN17004689
SRA SRX9633975

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

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