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Sample GSM1295706 Query DataSets for GSM1295706
Status Public on Dec 21, 2013
Title KD d6 replicate 2
Sample type RNA
Source name KD d6
Organism Mus musculus
Characteristics cell type: RGC-like NPC
treatment: Zrf1 KD
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 12.9903358
2 6.033214474
3 5.974355514
4 6.164624866
5 7.301554858
6 6.385711998
7 6.138702511
8 11.69548766
9 6.172122293
10 6.623943789
11 6.920399694
12 6.20106283
13 8.75928024
14 10.81270639
15 6.70064244
16 6.001830347
17 12.98581081
18 7.674456354
19 11.1439969
20 15.32880571

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.

Supplementary file Size Download File type/resource
GSM1295706_13_MA_1200252800514360_Cy3_KD_d6_2_TR_1_2.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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