|
Status |
Public on Apr 25, 2014 |
Title |
BJ-OKS-iG#5 |
Sample type |
SRA |
|
|
Source name |
iPS cell derived from BJ
|
Organism |
Homo sapiens |
Characteristics |
karyotype: Normal cell type: iPS cell derived from BJ
|
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-OKS-iG5.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 |
SRX149683 |
BioSample |
SAMN00998583 |