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| Status |
Public on Mar 01, 2020 |
| Title |
CHIP_P0_cortex_WT_RAD21_rep2 |
| Sample type |
SRA |
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| Source name |
Cortex neuron
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| Organism |
Mus musculus |
| Characteristics |
tissue: cortex
age: P0
line: WT
genotype: WT
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
4 × 106 of cells were cross-linked by 1% formaldehyde in 10% FBS/PBS for 10 min at room temperature. Cells were then lysed twice with ice-cold lysis buffer (20 mM Tris-HCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate and 1× protease inhibitors, pH 7.5) for 10 min with slow rotations.
The lysed cells were then sonicated to obtain DNA fragments of about 200-500 bp using the Biorupter system (high energy, with working time of 30 seconds and resting time of 30 seconds, 30 cycles). After removal of the insoluble debris, the lysate was incubated with specific antibodies against CTCF (07-729; Millipore), RAD21 (ab992; Abcam), or H3K27ac (ab4729; Abcam) and purified by protein A-agarose beads (16-157; Millipore). NIPBL ChIP-seq were from recently published data49. ChIP DNA was extracted and prepared for high throughput sequencing using a DNA library preparation kit for Illumina (NEB). ChIP-seq libraries were sequenced on a HiSeq X Ten Platform (Illumina).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Reads were mapped to the reference genome (GRCh37/hg19、NCBI37/mm9) or the modified genome with insertions using the Bowtie program.
Peaks were called by the MACS program (version 1.4.2) with a cutoff P value of 10−5.
Genome_build: UCSC hg19、NCBI37/mm9
Supplementary_files_format_and_content: zipped wig files include RPM values for each Sample
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| Submission date |
Oct 31, 2019 |
| Last update date |
Mar 03, 2020 |
| Contact name |
Xiao Ge |
| Organization name |
Shanghai JiaoTong University
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| Street address |
No. 800 Dongchuan Road
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| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE138646 |
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection |
| GSE139679 |
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [V] |
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| Relations |
| BioSample |
SAMN13170608 |
| SRA |
SRX7081382 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4145981_CHIP_P0_cortex_WT_RAD21_rep2.wig.gz |
287.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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