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Sample GSM866783 Query DataSets for GSM866783
Status Public on May 01, 2012
Title sh JMJD3 - TGFb, replicate 2
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 13.19299678
2 6.289153831
3 6.200737179
4 6.190059008
5 6.187858408
6 6.222927286
7 6.201107747
8 6.242805385
9 6.236898625
10 6.198150572
11 6.251800153
12 8.349441087
13 6.378054433
14 11.85862227
15 7.339811821
16 13.12799101
17 10.56131793
18 6.368509259
19 6.32317285
20 6.692797537

Total number of rows: 45220

Table truncated, full table size 773 Kbytes.




Supplementary file Size Download File type/resource
GSM866783_11_MA_1300252665510182_Cy3_18_sh2JMJD3-TGFb_1_3.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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