|
| Status |
Public on Jul 12, 2019 |
| Title |
chimp.iPSC.alter-medium.RNA.Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
chimp.iPSC.alter-medium.RNA
|
| Organism |
Pan troglodytes |
| Characteristics |
differentiation time: day00
cell type: chimp induced pluripotent stem cell
|
| Growth protocol |
Chimpanzee iPSCs were cultured on plates pre-coated with Matrigel (BD Biosciences) in a customized mTeSR1 medium (CTFR medium)19: mTeSR1 basal medium supplemented with FGF2 (Peprotech, 20ng/ml) and IWR1(Sigma, 2.5uM). Chimpanzee iPSCs 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 |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol according to protocol (Thermo Scientific, 15596-026). All libraries were constructed using standard illumina TruSeq LT library prep.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RLT_14
|
| 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 |
Jul 11, 2019 |
| Last update date |
Jul 12, 2019 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Street address |
9500 Gilman Dr.
|
| City |
San Diego |
| State/province |
CA |
| 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 |
SAMN12254136 |
| SRA |
SRX6430450 |
