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Sample GSM843789 Query DataSets for GSM843789
Status Public on Jan 06, 2012
Title ES KD33 biological replicate 2
Sample type RNA
Source name embryonic stem cells
Organism Mus musculus
Characteristics sample type: embryonic stem cells
treatment: Cbx7 depleted KD33
Extracted molecule total RNA
Extraction protocol Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol
Label Cy3
Label protocol 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)
Hybridization protocol After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).
Scan protocol The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
Data processing Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.
Submission date Dec 06, 2011
Last update date Jan 06, 2012
Contact name Luciano Di Croce
Phone +34933160132
Organization name Centre for Genomic Regulation
Street address Dr. Aiguader, 88
City Barcelona
ZIP/Postal code 08003
Country Spain
Platform ID GPL10333
Series (1)
GSE34191 Non-Overlapping Functions of the Polycomb group Cbx Family of Proteins in Embryonic Stem Cells

Data table header descriptions
VALUE normalized log2 intensity values

Data table
1 15.35996978
2 6.199218512
3 6.14646384
4 6.077480199
5 6.143075796
6 6.164733288
7 6.129558737
8 6.113322856
9 6.126662322
10 6.145918966
11 6.13040455
12 8.249304084
13 6.210078952
14 9.615898588
15 7.085841863
16 11.97171763
17 12.56490845
18 6.245805667
19 6.189793125
20 9.527216497

Total number of rows: 45220

Table truncated, full table size 770 Kbytes.

Supplementary file Size Download File type/resource
GSM843789_HM_1000252665510538_Cy3_33-2_1_4.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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