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| Status |
Public on Dec 22, 2020 |
| Title |
Bcells_H3K27ac_ChIPseq |
| Sample type |
SRA |
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| Source name |
Activated B cells, 3 days
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: B1-8hi
cell type: splenic B cells
chip antibody: H3K27ac
vendor (antibody): Abcam
catalog# (antibody): ab4729
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| Treatment protocol |
Splenic B cells were cultured in RPMI-1640 medium supplemented with 100 U/mL IL-2, 5 ng/mL IL-4, 1.5 ng/mL IL-5, 0.2 ng/mL CD40 ligand, 0.01 ng/mL NP-ficoll, 10% FBS 10mM HEPES, 1 mM Na-Pyruvate, 0.1 mM non-essential amino acids and penicilli/streptmycin. For PC4 transduction, retrovirus preparation and transduction with MSCV FLAG-PC4 were performed as descrived previously (Ochiai et al. Nature Immunology 13,300-307, 2012).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Activated B cells were fixed 1% formaldehyde, followed by quenching with 125mM of glycine. The cells were washed with ice-cold PBS and were lysed. The crosslinked chromatin was shared with a Bioruptor Sonicator (CosmoBio) and target protein-DNA complexes were isolated with antibody.
Purified ChIP DNA was carried for preparing DNA libraries, and clonally amplified on a flow cell and sequenced on HiSeq2500 (HiSeq Control Software v2.2.38, Illumina) with 51-mer paired-end sequence. Image analysis and base calling were performed using Real-Time Analysis Software (v1.18.61, Illumina).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
Basecalls performed using CASAVA version 1.8.
Tag sequences were aligned to the mm10 genome assembly using bowtie2-2.3.2.
Peaks were identified using the FindPeaks tool in the HOMER package with input DNA tags as background distribution.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files reporting ChIP-seq peaks with input DNA tags as background distribution
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| Submission date |
Feb 26, 2020 |
| Last update date |
Dec 22, 2020 |
| Contact name |
Kyoko Ochiai |
| E-mail(s) |
kochiai@med.tohoku.ac.jp
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| Organization name |
Tohoku University School of Medicine
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| Department |
Biochemistry
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| Street address |
2-1, Seiryo-machi, Aobaku
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| City |
Sendai |
| ZIP/Postal code |
980-8575 |
| Country |
Japan |
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| Platform ID |
GPL9185 |
| Series (2) |
| GSE145951 |
Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4 (ChIP-seq) |
| GSE145953 |
Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4 |
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| Relations |
| BioSample |
SAMN14211860 |
| SRA |
SRX7805525 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4340105_H3K27AcWT1_TAG.ucsc.bedGraph.gz |
14.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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