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| Status |
Public on Apr 06, 2017 |
| Title |
WT_H4acChIP |
| Sample type |
SRA |
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| Source name |
murine embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
passage: 13-16
cell line: E14
genotype/variation: WT
treatment: untreated
chip antibody: anti-H4ac (Millipore, Cat # 06-598, Lot # 2510372)
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| Treatment protocol |
None
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| Growth protocol |
E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIPseq, cells were crosslinked with 1% formaldehyde. Crosslinking was quenched with 125mM glycine, and the cell pellets were sonicated for ChIP.
ChIP samples were end-repaired, A-tailed, and barcoded adaptors were ligated. DNA purified using EconoSpin column on every steps. The adaptor ligated DNA was PCR amplified for 16 cycles with Phusion polymerase.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Untreated E14 ES cells
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| Data processing |
Single-end raw FastQ reads were collapsed, adaptor sequence were removed, and reads were mapped to the mouse mm10 genome using bowtie, allowing one mismatch. Aligned reads were used for downstream analysis using the “annotatePeaks” command in HOMER (Heinz et al., 2010) to make 20 bp bins over promoter proximal regions and summing the reads within each bin. Experiments were aligned over high quality (peak score > 6) promoter-proximal Tip60 peaks called from (Ravens et al., 2015). After anchoring mapped reads over the reference site, heatmaps for biological replicates were generated using Java Treeview.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph
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| Submission date |
Mar 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Fazzio |
| E-mail(s) |
Thomas.Fazzio@umassmed.edu
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| Organization name |
UMMS
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| Street address |
364 Plantation street
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE85505 |
KAT–independent gene regulation by Tip60 promotes ESC self-renewal but not pluripotency |
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| Relations |
| BioSample |
SAMN06564103 |
| SRA |
SRX2636608 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2535217_ESC_WT_H4acChIP.bedGraph.gz |
78.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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