|
| Status |
Public on Sep 19, 2011 |
| Title |
GM12878 Negative Control Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
GM12878 T7 control RIP RNA
|
| Organism |
Homo sapiens |
| Characteristics |
rip antibody: anti-bacteriophage coat protein T7
|
| Treatment protocol |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeSunyAlbanyGeneSt#TRACK_HTML
|
| Extracted molecule |
total RNA |
| Extraction protocol |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeSunyAlbanyGeneSt#TRACK_HTML
RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols. Antibodies specific to the RNA Binding Protein (RBP) in question were first coated onto protein A/G containing magnetic beads and then used to immunoprecipitate the targeted, endogenously-formed mRNP complexes. Antibody-coated beads were incubated/tumbled with cell lysate overnight in the cold followed by extensive rinsing and subsequent purification of associated RNA using Phenol/Chloroform extraction and ethanol precipitation.
|
| Label |
biotin
|
| Label protocol |
Affymetrix WT standard
|
| |
|
| Hybridization protocol |
Affymetrix Standard
|
| Scan protocol |
Affymetrix GeneChipScanner 30007G using Affymetrix Gene Chip Command Console v3.1
|
| Description |
Immunoprecipitated RNA as part of ribonucleoprotein complexes
09_G10_IP_GM12878_10222009_(HuGene-1_0-st-v1).CEL
|
| Data processing |
Agilent GeneSpringGX software (version 11.0) Iterative PLIER 16 with quantile normalization applied across replicates within replicate groups
|
| |
|
| Submission date |
Aug 29, 2011 |
| Last update date |
Nov 03, 2011 |
| Contact name |
Frank Doyle |
| Organization name |
UAlbany CNSE
|
| Department |
Nanobiology
|
| Lab |
Tenenbaum
|
| Street address |
257 Fuller Rd
|
| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12203 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE31716 |
ENCODE SUNY RNA Binding Protein GeneST Data for GM12878 |
| GSE31724 |
ENCODE SUNY RNA Binding Protein GeneST Data for various cell lines |
|
