|
| Status |
Public on Jul 09, 2019 |
| Title |
chimp.iPSC.mTeSR1.HiC.Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cell
|
| Organism |
Pan troglodytes |
| Characteristics |
differentiation time: day00
cell type: chimp.iPSC
|
| Growth protocol |
Chimpanzee and bonobo iPSCs were cultured on plates pre-coated with Matrigel (BD Biosciences) in commercial mTeSR1TM medium (Stemcell technology, 85850). Cells were passaged every 5-6 days with TrypLE (Life Technologies) at a split ratio of 1:10. ROCK inhibitor Y27632 (10uM) was added at least one hour prior to and 24 hours after passaging.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. All libraries were constructed using standard illumina TruSeq LT library prep.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
chimp.mt.hic on Series record
|
| 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,calJac3, panPan2,panTro6
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.
|
| |
|
| Submission date |
Jun 28, 2019 |
| Last update date |
Oct 22, 2024 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL23423 |
| 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 |
|
| Relations |
| BioSample |
SAMN12163260 |
| SRA |
SRX6384259 |
