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| Status |
Public on Jul 09, 2019 |
| Title |
day00.CTCF.Rep2 |
| Sample type |
SRA |
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| Source name |
Embryonic stem cell
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Embryonic stem cell
differentiation time: day00
genotype: H9 MLC2v:H2B
matched input: day00.Input.Batch2.Rep2
chip antibody: CTCF
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP-seq has been carried out as previously described (Jolma et al., 2013; Tuupanen et al., 2012; Yan et al., 2013). Briefly, 2 million cells were crosslinked with 1% formadehyde for 15 min at RT. The reaction was quenched by adding 125 mM of Glycine and incubating for 5 min at RT. Cells were lysed in RIPA buffer (10 mM TrisHCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (Roche). And chromatin was sonicated into short fragments (300-700 bp). The fragmented chromatin was incubated with antibodies to pull down the specific DNA bound TFs or histones. After intensive wash, DNA was purified and prepared as sequencing library using illumina Truseq LT kit. Several samples with different indexes were pooled together for 50 or 100 cycles of single read sequencing with illumina Hiseq 2500.
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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 |
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie2 for ATAC-seq, BWA for ChIP-seq and Hi-C, rnaSTAR for RNA-seq. Contacts for Hi-C data were stored in the juicer Hi-C format (could be opened with juicebox.jar provided by Aiden lab).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for ChIP-seq and input, juicer hic format for Hi-C data and normalized read per million kilobases (RPKM) for RNA-seq.
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| Submission date |
Jul 10, 2018 |
| Last update date |
Jul 11, 2019 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
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| Organization name |
Ludwig Institute for Cancer Research
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| Street address |
9500 Gilman Dr.
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| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE116862 |
Chromatin structure dynamics during human cardiomyocyte differention reveals a role of HERV-H in demarcating TAD boundaries. |
| GSE186958 |
Chromatin structure dynamics during human cardiomyocyte differention |
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| Relations |
| BioSample |
SAMN09637531 |
| SRA |
SRX4377124 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3263065_CTCF_D00_Rep2.rpkm.bw |
93.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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