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Sample GSM1232170 Query DataSets for GSM1232170
Status Public on Nov 25, 2016
Title ZIM_replicate3
Sample type RNA
 
Source name Choriodecidua, zone remote from the cervix
Organism Homo sapiens
Characteristics tissue: choriodecidua
zone: remote zone from the cervix
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues, firstly crushed in Trizol (Life Technologies, Carlsbad, CA), using a Qiagen RNeasy Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug of Total RNA using the Low Input Quick Amp Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Sureprint G3 Human GE 8*60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using GE1_107_Sep09 scanning protocol (Scan resolution 2um)
Description Gene expression in zone of intact morphology
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Sep 16, 2013
Last update date Nov 26, 2016
Contact name Céline Méhats
E-mail(s) celine.mehats@inserm.fr
Organization name Inserm
Department U1016
Street address 24 rue du Faubourg St jacques
City Paris
ZIP/Postal code 75014
Country France
 
Platform ID GPL13607
Series (1)
GSE50900 Gene profiling of the zone of altered morphology of choriodecidua overlying the cervix before labor

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
4 6.91028152
5 6.384263654
6 6.026778984
7 10.59256516
8 11.18013649
9 5.1098779
10 5.80818889
11 4.880149321
12 9.594073957
13 9.098556011
14 9.91231411
15 7.195895929
16 5.66625613
17 6.048738555
18 5.1098779
19 9.403968632
20 8.766636174
21 8.857044953
24 6.566546996
25 9.419501772

Total number of rows: 58717

Table truncated, full table size 1014 Kbytes.




Supplementary file Size Download File type/resource
GSM1232170_US11043872_252800416099_S01_GE1_107_Sep09_2_2.txt.gz 3.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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