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Sample GSM1013440 Query DataSets for GSM1013440
Status Public on Oct 04, 2012
Title shCTR 72 RA biological replicate 3
Sample type RNA
 
Source name embryonic stem cell
Organism Mus musculus
Characteristics tissue: embryonic stem cell
transfection: shCTR
treatment: 72 hours with 1uM retinoic acid
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 Wahs buffer 2 (Agilent).
Scan protocol Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT
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 Oct 02, 2012
Last update date Oct 04, 2012
Contact name Luciano Di Croce
E-mail(s) luciano.dicroce@crg.eu
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)
GSE41277 Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity

Data table header descriptions
ID_REF
VALUE normalized log2 intensity values

Data table
ID_REF VALUE
1 12.97359877
2 6.158504617
3 6.101676585
4 6.123591212
5 6.075182674
6 6.110265916
7 6.174280045
8 6.155177115
9 6.175478737
10 6.141882913
11 6.100572181
12 7.319477114
13 6.160796575
14 11.62047042
15 6.449296005
16 11.76092873
17 11.65171215
18 6.18048931
19 6.149955881
20 8.870531726

Total number of rows: 45220

Table truncated, full table size 770 Kbytes.




Supplementary file Size Download File type/resource
GSM1013440_06_MA_1400252665510292_Cy3_shCTR72RA_3_1_4.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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