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Sample GSM7225389 Query DataSets for GSM7225389
Status Public on Apr 17, 2024
Title nonPC_H3p3, rep1
Sample type SRA
 
Source name B cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: B cells
genotype: WT
chil antibody: H3.3 (4H2D7)
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 (https://doi.org/10.1038/protex.2018.122), 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 OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description plasma cell differentiation
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)
Library strategy: ChIL-seq
 
Submission date Apr 24, 2023
Last update date Apr 17, 2024
Contact name Yasuyuki Ohkawa
E-mail(s) yohkawa@bioreg.kyushu-u.ac.jp
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
Relations
BioSample SAMN34357467
SRA SRX20089830

Supplementary file Size Download File type/resource
GSM7225389_20220714_ex13_Ad63_nonPC_H3p3_F-1.bin100smth1000SE.CPM.bw 22.6 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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