|
| Status |
Public on Nov 17, 2014 |
| Title |
IMR90 iPS (RNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: embryonic stem cell
cell line: IMR90
|
| Treatment protocol |
hESCs and hiPSCs were passaged onto feeder free gelatin coated plates twice before harvesting RNA
|
| Growth protocol |
hESCs and hiPSCs were maintained in DME supplemented with 20% KSR, nonessential amino acids (Invitrogen), L-Glutamine (Mediatech), Penn/Strep, 2-mercaptoethanol with a feeder layer of MEFs as previously described (Shen et al., 2006).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using Trizol (Invitrogen) while DNA was isolated using PureLinkTM genomic DNA purification kit (Invitrogen).
Library construction was performed following Illumina manufacturer suggestions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ICF_normReadcounts.txt
|
| Data processing |
Supplementary_files_format_and_content: ICF_normReadcounts.txt matrix listing normalized read counts
Raw reads from the Illumina HiSeq2000 were mapped to the hg18 genome and Refseq genes using default parameters in BWA
Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression in all stages (average RPKM<0.1) were filtered out
Poisson statistics were performed on the read counts of genes that passed filtering
|
| |
|
| Submission date |
Jun 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Huang |
| Phone |
310-267-0438
|
| Organization name |
UCLA
|
| Department |
Human Genetics
|
| Lab |
Guoping Fan
|
| Street address |
Gonda BLDG Rm. 6554, P.O.Box 957088
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7088 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46030 |
Selective demethylation and altered gene expression are associated with ICF Syndrome in human induced pluripotent stem cells and mesenchymal stem cells |
|
| Relations |
| BioSample |
SAMN02842721 |
| SRA |
SRX576050 |
