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Sample GSM787600 Query DataSets for GSM787600
Status Public on Sep 19, 2011
Title HeLaS3 Negative Control Rep2
Sample type RNA
 
Source name HeLaS3 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_HeLa_G10_pool_06032010_(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)
GSE31719 ENCODE SUNY RNA Binding Protein GeneST Data for HeLaS3
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 6.3665433
7896738 6.3678613
7896740 5.4970703
7896742 8.201866
7896744 4.827652
7896746 8.118523
7896748 9.306118
7896750 5.636146
7896752 8.072957
7896754 6.660165
7896756 6.122649
7896759 8.988013
7896761 9.357566
7896779 7.9383593
7896798 10.155413
7896817 7.132884
7896822 9.014362
7896859 6.9126577
7896861 5.3423533
7896863 7.00227

Total number of rows: 28869

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM787600.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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