|
| Status |
Public on Apr 25, 2014 |
| Title |
Parent BJ cell |
| Sample type |
SRA |
| |
|
| Source name |
Human fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human fibroblast
|
| Growth protocol |
iPS cells and HUES9 cells were passaged on ES matrigel-coated plates and cultured in feeder-free condition with STO feeder conditioned medium prepared from ES culture medium containing KO-DME/20%KSR/NEAA/2-Mercaptoethanol/Pen/Strep/bFGF. BJ cells were cultured in DMEM/10%FBS/NEAA/Pyruvate/Pen/Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted from cultured cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina OLB-1.9.0 software used for basecalling.
For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71)
For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.
Genome_build: hg19
BJ.bed: hg19
|
| |
|
| Submission date |
May 25, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Hai-Ri Li |
| E-mail(s) |
hairili@ucsd.edu
|
| Phone |
858-534-4926
|
| Organization name |
University of California, San Diego
|
| Department |
Medicine
|
| Lab |
Dr. Francesca Telese
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE38265 |
mRNA expression in iPS cells generated by a synthetic self-replicative RNA |
|
| Relations |
| SRA |
SRX149679 |
| BioSample |
SAMN00998579 |
