|
| Status |
Public on Feb 01, 2012 |
| Title |
K562 |
| Sample type |
RNA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol
|
| Label |
Cy3
|
| Label protocol |
500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)
|
| |
|
| Hybridization protocol |
After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).
|
| Scan protocol |
Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT
|
| Data processing |
The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.
|
| |
|
| Submission date |
Jan 05, 2012 |
| Last update date |
Feb 01, 2012 |
| Contact name |
Rory Johnson |
| E-mail(s) |
[email protected]
|
| Organization name |
Centre for Genomic Regulation
|
| Department |
Bioinformatics and Genomics
|
| Street address |
Calle Dr Aiguader, 88
|
| City |
Barcelona |
| State/province |
Catalonia |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15094 |
| Series (1) |
| GSE34894 |
Long non-coding RNA expression in Human tissues and cell lines |
|
