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| Status |
Public on Dec 18, 2017 |
| Title |
dCD_BRG1_ChIPSeq.rep1 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: R1 ESC
strain: 129SV
genotype: MLL3/4 double catalytic dead
antibody: BRG1
antibody catalog #: ab110641
antibody vendor: Abcam
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| Growth protocol |
Cells were cultured on MEF feeder cells in serum free media (DMEM 10013-cv supplemented with 15% KSR, 2 mM L-glutamine, 100 μM nonessential amino acids, 50 μM beta-mercaptoethanol, 1000 units ml⁻¹ leukemia inhibitory factor (LIF), 100 units ml⁻¹ penicillin, and 100 μg ml⁻¹ streptomycin.) at 37°C with 5%CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked cells were processed by Covaris truChIP Chromatin Shearing kit and chromatin were sonicated to 300-500bp by Covaris M220. ChIP DNA and Input DNA were constucted into illumina Tru-seq libraries as previously described (Jian Yan et al., 2013), followed by size selection for 300-500bp.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
ChIP-seq sequencing data was trimmed and aligned to mm9(July 2007, NCBI37) by bwa (version 0.7.13-r1126). Unmapped, multimapped and PCR duplicates were removed by Picard(2.11.0).
ChIP seq peaks were called for each replicate and pooled data using MACS2(2.1.0.20150731) with default parameters. Pooled peaks that were found in both replicates were defined as reproducible peaks for each factor.
ChIP Fold enrichment over input was calculated by macs2 bdgcmp. Normalized ChIP signal was generated by UCSC tool bedGraphToBigWig. Averaged ChIP-seq fold enrichment over input at each reproducible peak was calculated using bigWigAvgOverBed.
Distal regions are peaks whose center are ± 2kb away from GENCODE transcript TSS. Using two fold difference cut off, distal regions were classified as “decreased”,”unhcnaged” and “increased” by comparing the fold enrichment over input in DCD to that in WT. If the fold enrichment of a region in DCD is less than half of that in WT, the region was defined as decreased.
Heatmap and aggregate profile of input normalized CHIP-seq signal were generated by deepTools 2.5.1.
Genome_build: mm9
Supplementary_files_format_and_content: Signal tracks were generated by bamCoverage 2.5.3 with parameters "--normalizeUsingRPKM -e 300 -bs 25 --smoothLength 75" (deepTools)
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| Submission date |
Oct 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bing Ren |
| Organization name |
University of California, San Diego School of Medicine
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| Street address |
9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE80049 |
Identification of H3 Lysine 4 monomethylation Associated Proteins at Mammalian Enhancers |
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| Relations |
| BioSample |
SAMN07775271 |
| SRA |
SRX3270964 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2808672_dCD_BRG1.rep1.bw |
272.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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