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Sample GSM787612 Query DataSets for GSM787612
Status Public on Sep 19, 2011
Title HepG2 Negative Control Rep2
Sample type RNA
 
Source name HepG2 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
ST_HEPG2_G10_0018_06162010_(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 Sep 19, 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)
GSE31720 ENCODE SUNY RNA Binding Protein GeneST Data for HepG2
GSE31724 ENCODE SUNY RNA Binding Protein GeneST Data for various cell lines

Data table header descriptions
ID_REF
VALUE log2 Iterative PLIER signal (quantile normalized within replicate groups)

Data table
ID_REF VALUE
7896736 5.879441
7896738 5.958259
7896740 6.4012346
7896742 8.706201
7896744 7.1077995
7896746 12.349723
7896748 11.298605
7896750 11.3400755
7896752 11.491589
7896754 6.6046567
7896756 7.5040903
7896759 7.602861
7896761 9.654924
7896779 8.830705
7896798 7.406171
7896817 8.961233
7896822 11.04357
7896859 7.897362
7896861 5.084493
7896863 6.9941897

Total number of rows: 28869

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM787612.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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