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Sample GSM945837 Query DataSets for GSM945837
Status Public on Dec 31, 2012
Title Olig2 Cells, PDGF/PTEN-deleted Glioma Ribosome-bound RNA, Replicate 1
Sample type RNA
 
Source name Olig2 Cells, PDGF/PTEN-deleted Glioma Ribosome-bound RNA, Replicate 1
Organism Mus musculus
Characteristics fraction: Ribosome-bound RNA
Extracted molecule total RNA
Extraction protocol For collection of total cellular RNA, normal brain or grossly-dissected tumor tissue was dissociated into a single cell suspension with papain and GFP+ cells were collected by FACS (Becton-Dickinson Aria Cell Sorter). Sorted cells were collected with Trizol-LS (Invitrogen), chloroform extracted, precipitated with sodium acetate in isopropanol overnight, and purified with Qiagen RNeasy MinElute Cleanup Kit. Ribosome-bound RNA was immunoprecipitated with anti-GFP conjugated magnetic beads from mechanically-homogenized tissue and purified as above. Tissue samples were divided equally for total and ribosome-bound RNA to generate paired datasets.
Label biotin
Label protocol Illumina TotalPrep RNA Amplification manufacturer protocol
 
Hybridization protocol Standard Illumina protocol
Scan protocol Standard Illumina protocol
Description Cre IP G121
Data processing Non-normalized data is background subtracted; Normalized data is background subtracted, filtered for only probes with detection p-value<0.05 in all samples, quantile normalized in Partek Genomics software and log2 transformed.
 
Submission date Jun 08, 2012
Last update date Dec 31, 2012
Contact name Karim Helmy
E-mail(s) karimhelmy@stanfordalumni.org
Organization name Memorial Sloan-Kettering Cancer Center
Street address 1275 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL6885
Series (1)
GSE38591 Identification of global alteration of translational regulation in glioma in vivo

Data table header descriptions
ID_REF
VALUE Normalized data
Cre IP G121 detection p-value

Data table
ID_REF VALUE Cre IP G121 detection p-value
ILMN_1212612 8.41806 0
ILMN_1212632 7.3548 0
ILMN_1212636 11.4136 0
ILMN_1212637 7.853 0
ILMN_1212648 8.70119 0
ILMN_1212653 9.7963 0
ILMN_1212672 9.22809 0
ILMN_1212693 7.45752 0
ILMN_1212703 7.62245 0
ILMN_1212720 9.224 0
ILMN_1212759 8.675 0
ILMN_1212791 4.31862 0.04261
ILMN_1212875 8.72084 0
ILMN_1212894 10.8602 0
ILMN_1212902 9.36359 0
ILMN_1212907 9.64557 0
ILMN_1212941 12.4446 0
ILMN_1212975 7.75046 0
ILMN_1212982 7.46761 0
ILMN_1212993 6.14517 0.00125

Total number of rows: 9653

Table truncated, full table size 220 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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