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Sample GSM866782 Query DataSets for GSM866782
Status Public on May 01, 2012
Title sh JMJD3 - TGFb, replicate 1
Sample type RNA
 
Source name sh2 JMJD3 - TGFb
Organism Mus musculus
Characteristics cell type: neural stem cells
knockdown: sh2 JMJD3
treatment: none
age: E12.5
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 110%PMT
The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
Description dissected out from embrionic cerebral cortex (E12.5). Cells are stably transfected with a JMJD3 shRNA.
Data processing Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.
 
Submission date Jan 26, 2012
Last update date May 01, 2012
Contact name Conchi EI
Organization name IBMB
Street address Baldiri Reixac 15
City Barcelona
ZIP/Postal code 08028
Country Spain
 
Platform ID GPL10333
Series (1)
GSE35361 JMJD3 is needed to regulate TGF beta responsive genes.

Data table header descriptions
ID_REF
VALUE normalized log2 intensity values

Data table
ID_REF VALUE
1 14.00684285
2 6.243738633
3 6.254438612
4 6.267185275
5 6.266923075
6 6.269467052
7 6.224695655
8 6.242782202
9 6.282924112
10 6.273689094
11 6.222423053
12 8.038892825
13 6.327727304
14 11.60101275
15 7.214415429
16 12.95382631
17 10.91433911
18 6.303204715
19 6.440960734
20 6.707944571

Total number of rows: 45220

Table truncated, full table size 773 Kbytes.




Supplementary file Size Download File type/resource
GSM866782_10_MA_1400252665510181_Cy3_17_sh2JMJSD3-TGFb_1_4.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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