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Sample GSM485412 Query DataSets for GSM485412
Status Public on Feb 28, 2010
Title NA19130_yale
Sample type SRA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell line: NA19130
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA19130
Growth protocol 37o in RPMI
Extracted molecule total RNA
Extraction protocol Total RNA from HapMap Yoruba lymphoblastoid cell lines was extracted using an RNeasy Mini Kit (Qiagen) and assessed using an Agilent Bioanalyzer. mRNA was then isolated with Dyna1 oligo-dT beads (Invitrogen) from 10 micrograms of total RNA. The mRNA was randomly fragmented using the RNA fragmentation kit from Ambion. First-strand cDNA synthesis was performed using random primers and SuperScriptII reverse-transcriptase (Invitrogen). This was followed by second-strand cDNA synthesis using DNA Polymerase I and RNaseH (Invitrogen). The short cDNA fragments from each sample were prepared into a library for Illumina sequencing. Briefly, the Illumina adaptor was ligated to the ends of the double-stranded cDNA fragments and a 200 bp size-selection of the final product was performed by gel-excision, following the Illumina-recommended protocol. 200 bp cDNA template molecules with the adaptor attached were enriched by PCR to create the final library.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description RNA-Seq
Data processing Mapped using MAQ v. 0.6.8
 
Submission date Dec 15, 2009
Last update date May 15, 2019
Contact name Joseph Pickrell
E-mail(s) pickrell@uchicago.edu
Organization name University of Chicago
Street address 920 E. 58th St.
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL9115
Series (1)
GSE19480 Understaning mechanisms underlying human gene expression variation with RNA sequencing
Relations
SRA SRX014579
BioSample SAMN00006706

Supplementary file Size Download File type/resource
GSM485412_NA19130_yale.map.gz 341.1 Mb (ftp)(http) MAP
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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