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Sample GSM546363 Query DataSets for GSM546363
Status Public on Jun 29, 2010
Title e11.5_placenta_rep4 [exon version]
Sample type RNA
 
Source name placenta, p11.5
Organism Mus musculus
Characteristics age: e11.5
tissue: placenta
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 GSM546318 (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 38.08586
4304921 41.40465
4304922 50.69122
4304923 136.31180
4304925 178.10666
4304927 41.51516
4304928 4826.54486
4304929 1227.19647
4304930 74.76866
4304931 88.86798
4304932 92.17713
4304933 44.62674
4304934 53.46450
4304935 45.60387
4304937 38.79816
4304938 174.47393
4304939 36.84288
4304940 56.75991
4304941 220.58797
4304942 313.53352

Total number of rows: 1236087

Table truncated, full table size 21019 Kbytes.




Supplementary file Size Download File type/resource
GSM546363_SR20080228MEX23.CEL.gz 37.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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