|
| Status |
Public on Jan 24, 2009 |
| Title |
GM12878_IP-PABP_1 |
| Sample type |
RNA |
| |
|
| Source name |
PABP-associated RNA
|
| Organism |
Homo sapiens |
| Characteristics |
GM12878
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
|
| Growth protocol |
http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#Cell_phenotype_study
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from Immunoprecipitated samples was isolated using phenol-chloroform and cleaned up on Qiagen Rneasy columns before QC on a bioanlyzer and a nanodrop spectrophotometer
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix WT protocol for Exon arrays
|
| |
|
| Hybridization protocol |
Standard Affymetrix WT protocol for Exon arrays
|
| Scan protocol |
Standard Affymetrix WT protocol for Exon arrays
|
| Description |
ST_14_GM12878_PABP_IP_10162008.CEL
|
| Data processing |
CEL files for each sample were processed using the apt-probeset-summarize binary provided by Affymetrix. One qualitative (DABG) and two quantitative (RMA, PLIER) measures of expression were derived for each gene-level metaprobeset on the chips using command line parameters (see Workflow PDF linked to GSE14535 for full details).
|
| |
|
| Submission date |
Jan 23, 2009 |
| Last update date |
Jan 23, 2009 |
| Contact name |
Sridar V Chittur |
| E-mail(s) |
schittur@albany.edu
|
| Phone |
518-591-7215
|
| Organization name |
SUNY-University at Albany
|
| Department |
Center for Functional Genomics
|
| Lab |
Microarray Core
|
| Street address |
One Discovery Drive, CRC 342G
|
| City |
Rensselaer |
| State/province |
NY |
| ZIP/Postal code |
12144 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE14535 |
mRNP-mRNA Association Map (Tier I - G10, HuR, Imp, PABP) |
|
