|
| Status |
Public on Aug 29, 2012 |
| Title |
MCF-7_CTCF_shRNA_knockdown_B3 |
| Sample type |
RNA |
| |
|
| Source name |
mammary gland, adenocarcinoma, CTCF knockdown using shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: mammary gland, adenocarcinoma, CTCF knockdown using shRNA
|
| Growth protocol |
Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted from cell pellets using Trizol protocol
|
| Label |
biotin
|
| Label protocol |
1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 ST arrays
|
| |
|
| Hybridization protocol |
Standard Affymetrix WT protocol for Exon 1.0 ST arrays
|
| Scan protocol |
Standard Affymetrix WT protocol for Exon 1.0 ST arrays
|
| Description |
.bed file contains gene-level normalized expression values
|
| Data processing |
Probesets flagged as cross-hybridizing were removed. Probesets were assigned to genes based on the GENCODE v10 annotation (July 2011). To normalize, we first classified each exon as constitutive, meaning present in all annotated isoforms, or not constitutive for each gene, reasoning these would be the most robust across celltypes. For genes with at least 4 constitutive probesets, only constitutive probesets were used to normalize. For all other genes, including all non-protein-coding genes, we sused all probesets that mapped to the gene. To normalize, we used Affymetrix Power Tools (APT) with the chipstream command “rma-bg, med-norm, pm-gcbg, med-polish”. This chipstream calls for an RMA normalization with gc-background correction using antigenomic background probes. We used an ComBat to correct for batch effects.
|
| |
|
| Submission date |
Aug 28, 2012 |
| Last update date |
Aug 30, 2012 |
| Contact name |
Sridar V Chittur |
| E-mail(s) |
[email protected]
|
| 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 |
GPL15997 |
| Series (1) |
| GSE15805 |
Duke-UNC-Texas-EBI ENCODE expression project |
|
