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| Status |
Public on Feb 16, 2018 |
| Title |
mESC_Rsf1_ubH2Adel_ChIP-seq_rep1 |
| Sample type |
SRA |
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| Source name |
mouse embryonic stem cell
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| Organism |
Mus musculus |
| Characteristics |
genotype: Rsf1Flag Knockin with RNF2 KO
strain: C57BL/6 X 129/sv
cell line: v6.5
passages: 15-18
chip antibody: Flag Beads (Sigma, A2220)
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| Growth protocol |
DMEM medium (High glucose, Gibco MT-10-013) supplemented with 50unit/ml penicillin and streptomycin (Life technologies, 15070-063), 18% murine ESC defined FBS (Thermo Scientific, SH30070.03E), 2mM L-glutamine (Cellgro, 25-005-CI), 1mM sodium pyruvate (Gibco, 11360-070), 1X nonessential amino acids (Cellgro, 25-025-CI, 100X stock), 1X nucleoside (Millipore, ES-008-D, 100X stock), 0.007% β-mercaptoethanol (Fisher, O3446I), and 1000unit/ml mLIF (Millipore, ESGRO) on irradiated mouse embryonic fibroblasts (Millipore, PMEF-NL) or 0.1% gelatin coated plates
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde. Chromatin was disrupted into 100-250 bp fragments by sonication and precipitated using antibody and protein A beads as indicated in the text and protein A beads. After elution from the beads and reversing the cross-linking, the DNA fragments in immunoprecipitates were extracted with phenol/chloroform and recovered by ethanol precipitation.
Immunoprecipitated DNA was ligated with 3’- and 5’-adapters for amplification and sequencing by using Illumina II.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
For RNA-seq data, reads were mapped to hg19 or mm10 using STAR version 2.5.1b. Differentially expressed genes (q-value≤0.05) were identified with Cuffdiff. The log2 fold change is a direct output from Cuffdiff. For visualization, the mapped reads were converted into BedGraph format using BEDTools. For ChIP-seq data, reads were mapped to hg19 or mm10 using bowtie version 1.1.2. Bam files are sorted by Samtools and PCR duplicates were removed using Picard (http://picard.sourceforge.net). Peak calling was perform using MACS-1.4.2. For MNase-seq, Reads were analyzed and profiled using Danpos.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample or wig file
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| Submission date |
Jan 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hengbin Wang |
| E-mail(s) |
hbwang@uab.edu
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| Phone |
2059345286
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| Organization name |
University of Alabama at Birmingham
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| Department |
Biochemistry and Molecular Genetics
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| Lab |
Hengbin Wang
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| Street address |
720 20th St S Kaul Bldg 430
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| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platform ID |
GPL9250 |
| Series (1) |
| GSE93090 |
Role of remodeling and spacing factor 1 in histone H2A ubiquitination mediated gene silencing |
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| Relations |
| BioSample |
SAMN06198671 |
| SRA |
SRX2458511 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2443540_mESC_Rsf1_ubH2Adel_ChIP-seq_rep1.wig.gz |
476.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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