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| Status |
Public on Apr 17, 2024 |
| Title |
nonPC_H3p3, rep2 |
| Sample type |
SRA |
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| Source name |
B cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: B cells
genotype: WT
chil antibody: H3.3 (4H2D7)
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
plasma cell differentiation
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| 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
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| Submission date |
Apr 24, 2023 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Yasuyuki Ohkawa |
| E-mail(s) |
yohkawa@bioreg.kyushu-u.ac.jp
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| Organization name |
Medical Institute of Bioregulation
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| Lab |
Division of Transcriptomics
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| Street address |
3-1-1 Maidashi
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| City |
Fukuoka |
| ZIP/Postal code |
8128582 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE230496 |
Epigenomic profiling by ATAC-seq and ChIL-seq in B cells and plasma cells |
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| Relations |
| BioSample |
SAMN34357466 |
| SRA |
SRX20089831 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7225390_ChIL_exp14_nonPC_H3p3_1F_Ad49.bam.bin100smth1000SE.CPM.bw |
34.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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