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Sample GSM7225370 Query DataSets for GSM7225370
Status Public on Apr 17, 2024
Title Naive, rep2
Sample type SRA
Source name B cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: B cells
genotype: WT
Extracted molecule genomic DNA
Extraction protocol For B cell isolation, splenic B cells were purified by the negative selection of CD43+ cells with anti-CD43 magnetic beads (Militenyi Biotec). The purified B cell population was>95% positive for CD19 staining. Cell sorting was performed on FACSMelody (BD Biosciences) to isolate the following populations: activated B cells (CD138lowB220hi) ; plasma cells (CD138hiB220low) and retrovirus-infected cells (GFP+) .For B cell stimulation assays, purified B cells were cultured in RPMI 1640 medium. For plasma cell differentiation, B cells were stimulated with 5 μg/ml of lipopolysaccharide (LPS).
Assay for transposase-accessible chromatin sequencing (ATAC-seq): ATAC-seq was performed following published protocol (Corces, M. et al., Nat Methods, 2017). 50,000 cells were used for each library.
Chromatin integration labelling (ChIL): ChIL-seq for B cells was performed described previously (, except following. Cells were biotinylated for 30 min at 4°C with 1mg/ml sulfoNHS-SS-biotin in PBS and plated on streptavidin-treated 96-well plates (Thermo Fisher Scientific). After fixed with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 5min at room temperature, fixation was stopped with 1 M Glycine/HCl.
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
Description B cells
Data processing After sequencing, reads were cleaned by trim_galore (version0.6.10) and mapped to mm10 with Bowtie2(version 2.3.1).
Replicate samples were merged and peaks were identified by using MACS2(ChIL: -q 0.01 --nomodel –nolambda, ATAC: -q 0.01)
Bigwig files were prepared using deeptools with following options "--binSize 100 --centerReads --normalizeUsing CPM" for ATAC-seq and "--smoothLength 1000 --binSize 100 --normalizeUsing CPM" for ChIL-seq.
Assembly: mm10
Supplementary files format and content: peak summit files(.bed), bigwig files(.bigwig)
Submission date Apr 24, 2023
Last update date Apr 17, 2024
Contact name Yasuyuki Ohkawa
Organization name Medical Institute of Bioregulation
Lab Division of Transcriptomics
Street address 3-1-1 Maidashi
City Fukuoka
ZIP/Postal code 8128582
Country Japan
Platform ID GPL24247
Series (1)
GSE230496 Epigenomic profiling by ATAC-seq and ChIL-seq in B cells and plasma cells
BioSample SAMN34357486
SRA SRX20089811

Supplementary file Size Download File type/resource 33.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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