|
| Status |
Public on Nov 25, 2020 |
| Title |
ΔZF9-11_Syn1-6_Rad21_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: F123 ESC
strain: F1 hybrid (castaneus x S129/SvJae)
chip antibody: ab992
genotype: Syn1-6-insertion, CTCF <delta>ZF9-11
|
| Growth protocol |
Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Inserted sequence was add to the mm10 genome. And a customized mm10 genome was indexed by bowtie2-build
ChIP-seq sequencing data was trimmed and aligned to mm10 by bowtie2. Unmapped, multimapped and PCR duplicates were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Signal tracks were generated by bamCoverage with parameters "--normalizeUsingRPKM -bs 50 --smoothLength 150" (deepTools)
|
| |
|
| Submission date |
Nov 24, 2020 |
| Last update date |
Nov 25, 2020 |
| Contact name |
Bing Ren |
| Organization name |
University of California, San Diego School of Medicine
|
| Street address |
9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE153400 |
CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains [ChIP-seq] |
| GSE153403 |
CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains |
|
| Relations |
| BioSample |
SAMN16882035 |
| SRA |
SRX9567815 |
