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Sample GSM866778 Query DataSets for GSM866778
Status Public on May 01, 2012
Title sh control - TGFb, replicate 3
Sample type RNA
 
Source name sh control - TGFb
Organism Mus musculus
Characteristics cell type: neural stem cells
knockdown: control
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 random 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 12.71982315
2 6.310717457
3 6.366007722
4 6.27431713
5 6.297995281
6 6.322216968
7 6.303274741
8 6.304516474
9 6.366875027
10 6.325757801
11 6.332965896
12 8.376519602
13 6.479742313
14 11.72576243
15 7.092673609
16 13.28463758
17 10.64707319
18 6.43523188
19 6.305714064
20 7.489256482

Total number of rows: 45220

Table truncated, full table size 773 Kbytes.




Supplementary file Size Download File type/resource
GSM866778_03_MA_1300252665510183_Cy3_4_shctrl-TGFb_1_3.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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