NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM850172 Query DataSets for GSM850172
Status Public on Feb 16, 2012
Title Hela_hnRNPU_RNAseq_control
Sample type SRA
 
Source name HeLa cells
Organism Homo sapiens
Characteristics cell line: HeLa
transfection: Control
Treatment protocol Transfection of control siRNA
Growth protocol HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) with 10% newborn bovine serum plus 100 U penicillin /streptomycin (Gibico) at 37°C in 5% CO2.
Extracted molecule polyA RNA
Extraction protocol Total RNAs were extracted by Trizol from treated HeLa cells and polyA RNAs were enriched by oligod(T) selection. After fragmentation, mRNAs were reversely transcribed to cDNA with Superscript II in the presence of random primer. After RNase H digestion, the second strand cDNA was synthesized by DNA pol I followed by adaptor ligation. Size-selected PCR products were sequenced by Illumila Genome Analyzer II.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description Control cells
Data processing Hela_hnRNPU_RNAseq_control.bed; genome build: hg18
Paired-end reads were separately mapped into a custom Bowtie index, which was built from UCSC knownGenes (hg18) not including introns. Under the constraint of the insert size, only the paired-end reads whose two ends are about 50 nt apart on the same gene were kept. For each pair, the coordinates of the two end reads were mapped back to the genome based on its gene's genomic location, and then joined together. Only the pair-end reads with one unique genomic location were kept.
 
Submission date Dec 16, 2011
Last update date May 15, 2019
Contact name Xiang-Dong Fu
Organization name UC San Diego
Department CMM
Lab George Palade Laboratories
Street address 9500 Gilman Drive, Room 231
City La Jolla
State/province CA
ZIP/Postal code 92093-0651
Country USA
 
Platform ID GPL9115
Series (1)
GSE34491 Nuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation
Relations
SRA SRX111920
BioSample SAMN00766232

Supplementary file Size Download File type/resource
GSM850172_Hela_hnRNPU_RNAseq_control.bed.gz 159.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap