|
| Status |
Public on Jul 28, 2009 |
| Title |
HepG2_RCyP+ |
| Sample type |
RNA |
| |
|
| Source name |
BD SMARTTM RACE cDNA – HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
age: 15 years old caucasian male
tissue: HepG2 cell line
|
| Growth protocol |
11 tissues poly A+ RNA was purchased and 5 cell lines were grown as suggested by ATCC
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
see Kapranov, et al Science 2002
|
| Label |
biotin
|
| Label protocol |
2 micrograms of polyA+ RNA were converted into double-stranded cDNA essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.
|
| |
|
| Hybridization protocol |
2 micrograms of double-stranded cDNA were labeled and hybridized to Affymetrix tiling arrays containing probes against non-repepetitive portions of human chromosomes 21 and 22 essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.
|
| Scan protocol |
Arrays were scanned on Affymetrix GCS3000 scanner
|
| Description |
includes cytoplasmic RNA
Single chip x 2 tech reps, each chromosome placed in separate file
|
| Data processing |
See supplement materials of Djebali, S, et al (2009) Nature in press
Bar files generated with proprietary software (almost identical to Affymetrix TAS). Bandwidth = 0, Normalization target= 330
|
| |
|
| Submission date |
Jul 27, 2009 |
| Last update date |
Jul 28, 2009 |
| Contact name |
Chris Zaleski |
| Organization name |
Cold Spring Harbor Labs
|
| Lab |
Gingeras
|
| Street address |
500 Sunnyside Blvd
|
| City |
Woodbury |
| State/province |
NY |
| ZIP/Postal code |
11797 |
| Country |
USA |
| |
|
| Platform ID |
GPL5715 |
| Series (1) |
| GSE17358 |
Transcriptional termini of genes on chromosomes 21-22 (RNA mapping) |
|
