|
| Status |
Public on May 30, 2018 |
| Title |
Rabbit iPS cells rbEKA-high cell line culture replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Rabbit iPS cells rbEKA-high cell line culture replicate
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
cell features: Rabbit B19-EOS iPS cells further transfected with a piggy Bac vector containing human KLF2 and KLF4
|
| 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.
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| |
|
| 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 |
rbEKA-high-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 |
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