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Sample GSM1232171 Query DataSets for GSM1232171
Status Public on Nov 25, 2016
Title ZAM_replicate1
Sample type RNA
Source name Choriodecidua, zone overlying the cervix
Organism Homo sapiens
Characteristics tissue: choriodecidua
zone: overlying 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 altered morphology
Data processing The scanned images were analyzed with Feature Extraction Software (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
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
VALUE Normalized signal intensity

Data table
4 7.521854652
5 6.638301438
6 6.335968761
7 10.64527479
8 9.82640132
9 5.68973845
10 6.430994081
11 5.367454272
12 9.965350037
13 9.557844759
14 9.036033589
15 7.454908305
16 5.563230778
17 6.75531999
18 5.30496294
19 9.507611083
20 8.9663585
21 9.799468972
24 7.008791417
25 9.846455258

Total number of rows: 58717

Table truncated, full table size 1016 Kbytes.

Supplementary file Size Download File type/resource
GSM1232171_US92003687_252800412571_S01_GE1_107_Sep09_2_4_2_.txt.gz 3.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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