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Sample GSM1485039 Query DataSets for GSM1485039
Status Public on May 21, 2015
Title Repl.2_Area19 Outer Subventricular Zone
Sample type RNA
 
Source name Repl.2_Area19 Outer Subventricular Zone
Organism Mustela putorius furo
Characteristics area: 19
zone: outer subventricular
tissue: Cerebral cortex
age: Postnatal day 2
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNeasy Mini RNA Purification kit (QUIAGEN, Cat. No. 74104) following the manufacturer's recommendations. The protocol includes cell lysis and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) 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 1.5 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-036832 Ferret_44K_v3 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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description 2A19OSVZ
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Aug 22, 2014
Last update date May 21, 2015
Contact name Victor Borrell
E-mail(s) vborrell@umh.es
Organization name CSIC
Department Institute of Neuroscience
Lab 221
Street address Av Ramon y Cajal s/n
City San Juan de Alicante
State/province Alicante
ZIP/Postal code 03550
Country Spain
 
Platform ID GPL19111
Series (1)
GSE60687 Sharp changes in gene expression levels along germinal layers distinguish the development of gyrencephaly

Supplementary file Size Download File type/resource
GSM1485039_US92603698_253683210004_S01_GE1_107_Sep09_1_3.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data are available on Series record

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