|
| Status |
Public on Mar 24, 2006 |
| Title |
plus 100nM RA treatment, 24h, replicate 2 (affy) |
| Sample type |
RNA |
| |
|
| Source name |
E14TG2a mouse embroyonic stem cells (ATCC, CRL-1841)
|
| Organism |
Mus musculus |
| Characteristics |
mouse embryonic stem cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from Mouse embryonic stem cells with 100nM all-trans retinoic acid induction for 24h were extracted using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).
|
| Label |
biotin
|
| Label protocol |
10 micrograms of total RNA was dephosphorylated with shrimp alkaline phosphatase (SAP, Invitrogen; 37degrees C, 40 min), followed by SAP inactivation (65degrees C, 40 min). The dephosphorylated RNA was biotin end-labeled (NEN biotin-N4 û CTP, NEL-510) with T4 RNA ligase (100 U/ml) in the presence of 40% polyethylene glycol (PEG) (37degrees C, 2 h).
|
| |
|
| Hybridization protocol |
All Chip hybridization, processing and scanning was done according to standard Affymetrix protocols.
|
| Scan protocol |
standard Affymetrix procedures
|
| Description |
plus 100nM RA treatment, 24h, replicate 2
|
| Data processing |
Raw data from a scanner consist of probe level data. A probe set contains 15 probe pairs and each probe pair consists of a perfect match and a mismatch probe. Affymetrix MAS version 5 was used to produce signal and signal detection calls. The resulting signals were log-transformed with base 2. A linear normalization with trimmed mean was employed to normalize signals across different experimental conditions. Mean signals of duplicate chips in each group were used for fold change computation. One-way analysis of variance was conducted and planned pairwise comparisons were performed for each miRNA with respect to Day 0. All the statistical computations were conducted using SAS« and S-Plus«. Data extraction and processing protocols were done on the Agilent scanner for Affymetrix(www.affymetrix.com). All Normalizations, transformations and data selection procedures and parameters were done using Affymetrix MAS.5 and GECOS software and algorithm (www.affymetrix.com)
|
| |
|
| Submission date |
Mar 21, 2006 |
| Last update date |
Mar 23, 2006 |
| Contact name |
Bing Lim |
| E-mail(s) |
limb1@gis.a-star.edu.sg
|
| Phone |
+65 64788156
|
| Fax |
+65 64789005
|
| URL |
http://www.gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Department |
Stem Cell and Developmental Biology
|
| Lab |
Stem Cell and Developmental Biology
|
| Street address |
60 Biopolis street, #02-01 Genome
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL3576 |
| Series (1) |
| GSE4522 |
MicroRNA-134 Modulates Mouse Embryonic Stem Cell Differentiation |
|
