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Sample GSM1295704 Query DataSets for GSM1295704
Status Public on Dec 21, 2013
Title Control d6 replicate 4
Sample type RNA
Source name Control d6
Organism Mus musculus
Characteristics cell type: RGC-like NPC
treatment: control
Extracted molecule total RNA
Extraction protocol Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol
Label Cy3
Label protocol 100 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 LowInputQuick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)
Hybridization protocol After fragmentation, 600 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 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 Dec 20, 2013
Last update date Dec 21, 2013
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 GPL13912
Series (2)
GSE53541 Zrf1 is required to establish and maintain neural progenitor identity (mRNA array)
GSE53542 Zrf1 is required to establish and maintain neural progenitor identity

Data table header descriptions
VALUE normalized log2 intensity values

Data table
1 12.77937603
2 6.242506609
3 6.218393609
4 6.443762817
5 7.340062413
6 6.542745589
7 6.418733649
8 11.65193699
9 6.369902853
10 6.842594498
11 7.616274257
12 6.292772576
13 9.272962844
14 11.47766202
15 7.069427665
16 6.299404586
17 13.39475785
18 7.861709586
19 10.96783921
20 16.36334774

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.

Supplementary file Size Download File type/resource
GSM1295704_11_MA_2300252800514360_Cy3_Ctrl_d6_4_2_3.txt.gz 11.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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