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| Status |
Public on Feb 28, 2010 |
| Title |
NA19257_argonne |
| Sample type |
SRA |
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| Source name |
lymphoblastoid cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: NA19257
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| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA19257
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| Growth protocol |
37o in RPMI
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
RNA-Seq
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| Data processing |
Mapped using MAQ v. 0.6.8
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| Submission date |
Dec 15, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph Pickrell |
| E-mail(s) |
[email protected]
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| Organization name |
University of Chicago
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| Street address |
920 E. 58th St.
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE19480 |
Understaning mechanisms underlying human gene expression variation with RNA sequencing |
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| Relations |
| SRA |
SRX014606 |
| BioSample |
SAMN00006733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM485439_NA19257_argonne.map.gz |
309.3 Mb |
(ftp)(http) |
MAP |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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