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Sample GSM546345 Query DataSets for GSM546345
Status Public on Jun 29, 2010
Title e9.5_embryo_rep1 [exon version]
Sample type RNA
 
Source name embryo, e9.5
Organism Mus musculus
Characteristics age: e9.5
tissue: embryo
strain: C57BL/6J
Treatment protocol Embryos for RNA isolation were stored in RNAlater (Ambion) prior to extraction.
Growth protocol To generate embryos, C57BL/6J females were placed with C57BL/6J males overnight and checked for the presence of a vaginal plug in the morning. The day that a plug was detected was considered embryonic day (E) 0.5. All mouse breeding and manipulations were performed in accordance with the Canadian Council on Animal Research. Embryos were collected between E6.5 – E11.5 for RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TriZOL (Invitrogen) according to the manufacturer's instructions.
Label biotin
Label protocol cDNA was synthesized using the GeneChip Whole Transcript Sense Target Labeling and Control Reagents kit (Affymetrix) on 1 µg of total RNA treated with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen). This sense cDNA was then labeled using the GeneChip WT Terminal labeling kit (Affymetrix). All the protocols used were provided by the manufacturers.
 
Hybridization protocol 5 micrograms of biotinylated target was incubated with the GeneChip Human Exon 1.0 ST array (Affymetrix) at 45°C for 16–20 h. After hybridization, nonspecifically bound material was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).
Scan protocol The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).
Data processing Affymetrix Power Tools and PLIER, on core PS and MPS only. For more info, refer to Revil, T. et al. 2010. BMC Genomics.
probe group file MoEx-1_0-st-v1.r2.pgf
meta-probeset file MoEx-1_0-st-v1.r2.dt1.mm8.core.mps
 
Submission date May 24, 2010
Last update date Jun 29, 2010
Contact name Timothee Revil
Organization name McGill University
Department Human Genetics
Lab Loydie Majewska
Street address 4060 Ste-Catherine W PT420
City Montreal
State/province Quebec
ZIP/Postal code H3Z2Z3
Country Canada
 
Platform ID GPL6193
Series (1)
GSE21971 Alternative splicing is frequent during early embryonic development in mouse
Relations
Alternative to GSM546300 (gene-level)

Data table header descriptions
ID_REF
VALUE Normalized by the whole gene expression level estimated by the PLIER algorithm

Data table
ID_REF VALUE
4304920 38.00078
4304921 30.56905
4304922 44.71946
4304923 156.43156
4304925 347.66995
4304927 51.72553
4304928 5705.10878
4304929 792.34201
4304930 55.47903
4304931 74.75956
4304932 100.83203
4304933 52.84823
4304934 56.49804
4304935 44.65171
4304937 80.39311
4304938 328.38708
4304939 33.43354
4304940 62.11583
4304941 211.10598
4304942 308.10020

Total number of rows: 1236087

Table truncated, full table size 21023 Kbytes.




Supplementary file Size Download File type/resource
GSM546345_SR20080228MEX06.CEL.gz 37.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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