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Sample GSM546346 Query DataSets for GSM546346
Status Public on Jun 29, 2010
Title e9.5_embryo_rep2 [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 GSM546301 (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 40.48136
4304921 34.17147
4304922 47.68542
4304923 70.05212
4304925 865.27802
4304927 46.02076
4304928 4247.32567
4304929 827.21077
4304930 63.02254
4304931 97.47203
4304932 102.01272
4304933 40.48604
4304934 50.44787
4304935 49.27456
4304937 61.70077
4304938 436.54684
4304939 40.93000
4304940 72.76384
4304941 183.18471
4304942 268.22691

Total number of rows: 1236087

Table truncated, full table size 21021 Kbytes.




Supplementary file Size Download File type/resource
GSM546346_SR20080228MEX07.CEL.gz 37.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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