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Sample GSM2646505 Query DataSets for GSM2646505
Status Public on May 30, 2018
Title Adult Rabbit Fibroblast - culture replicate 1
Sample type RNA
 
Source name Adult Rabbit Fibroblast - culture replicate
Organism Oryctolagus cuniculus
Characteristics cell features: Adult rabbit fibroblasts
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The protocol includes a 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 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling 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 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x 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 a Rabbit Agilent Custom Gene Expression Oligo Microarrays (G4102A) 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.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm).
Description RbF-1
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107 and Grid: 037293_D_F_20111104). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Jun 01, 2017
Last update date May 30, 2018
Contact name Jouneau Luc
E-mail(s) luc.jouneau@inrae.fr
Organization name INRA
Lab VIM
Street address Domaine de Vilvert
City Jouy-en-Josas
ZIP/Postal code 78352
Country France
 
Platform ID GPL18913
Series (1)
GSE99562 Reprogramming of rabbit induced pluripotent stem cells toward Inner Cell Mass cells and chimeric competency with Krüppel-like factors

Data table header descriptions
ID_REF
VALUE normalised by the median after log transformation

Data table
ID_REF VALUE
GE_BrightCorner 10.19967502
DarkCorner -1.832477883
A_04_P101083 -1.831123088
CUST_12537_PI427147524 3.824030956
A_04_P079278 -1.733825887
A_04_P091977 3.011738836
A_04_P061278 0.787006277
A_04_P065882 3.232961663
CUST_2599_PI427147524 -1.517497711
CUST_3344_PI427147524 1.413045742
A_04_P076582 -1.86507042
A_04_P017436 7.022947966
CUST_4164_PI427147524 -1.179583421
CUST_4482_PI427147524 0.737774957
CUST_6807_PI427147524 -1.620819306
CUST_7853_PI427147524 2.530340355
CUST_1375_PI427147524 -0.427696467
A_04_P074145 -1.59917636
CUST_5913_PI427147524 5.178999646
CUST_332_PI428255556 -0.326587876

Total number of rows: 42145

Table truncated, full table size 1170 Kbytes.




Supplementary file Size Download File type/resource
GSM2646505_RbF-1_254242110038_201407011023_S01_GE1_107_Sep09_1_3.txt.gz 10.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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