|
| Status |
Public on Nov 01, 2011 |
| Title |
NTERA-2cl.D1-DS14575 |
| Sample type |
RNA |
| |
|
| Source name |
Malignant pluripotent embryonal carcinoma, NTERA-2 cl.D1 (PMID: 6694356)
|
| Organism |
Homo sapiens |
| Characteristics |
lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
cell: NT2-D1
cell organism: human
cell description: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356)
cell karyotype: cancer
cell lineage: inner cell mass
cell sex: M
labexpid: RS19006
replicate: 2
|
| Biomaterial provider |
ATCC;CRL-1973
|
| Growth protocol |
Followed vendor recommendations for growth protocol/media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
|
| Label |
biotin
|
| Label protocol |
A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
|
| |
|
| Hybridization protocol |
Hybridizations were carried out according the manufacturer (Affymetrix) protocol
|
| Scan protocol |
Affymterix Gene Chip Scanner 3000
|
| Description |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwAffyExonArray
|
| Data processing |
Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
HuEx-1_0-st-v2.r2.pgf
quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
|
| |
|
| Submission date |
Oct 31, 2011 |
| Last update date |
Apr 23, 2013 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
encode-help@lists.stanford.edu
|
| Organization name |
ENCODE DCC
|
| Street address |
300 Pasteur Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE19090 |
Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types |
|
