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Sample GSM238540 Query DataSets for GSM238540
Status Public on Jan 13, 2008
Title NA07056 growth 3.
Sample type RNA
 
Source name CEU NA07056 Biological Growth 3
Organism Homo sapiens
Characteristics Gender: female, Cell-type: lymphoblasts
GM07056_03
Coriell cell line repository identifier:GM07056
Biomaterial provider Coriell Cell Repositories
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM07056
Treatment protocol Cells were harvested at a density of 0.8-1.1 x 10e6 cells/mL. Cells were then resuspended and lysed in TRIzol reagent
Growth protocol Cells were grown at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 15% heat-inactivated fetal bovine serum, 2 mM L-glutamine and penicillin/streptomycin
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinlabelled target for the microarray experiment were prepared using 1 ug of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix).
 
Hybridization protocol Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).
Description Probeset expression data from NA07056 growth 3
Data processing The data were analyzed with Affymetrix Power Tools package using Affymetrix default analysis settings and sketch quantile as normalization method.
 
Submission date Oct 18, 2007
Last update date Aug 14, 2011
Contact name Tony Kwan
E-mail(s) tony.kwan@mcgill.ca
Phone 514-398-3311
Organization name McGill University
Department Human Genetics
Street address 740 Dr. Penfield
City Montreal
State/province Quebec
ZIP/Postal code H3A 0G1
Country Canada
 
Platform ID GPL5175
Series (1)
GSE9372 Genome-wide analysis of transcript isoform variation in humans

Data table header descriptions
ID_REF transcript cluster identifier
VALUE PLIER calculated probeset and metaprobeset signal intensity
DABG Detection above background p-value

Data table
ID_REF VALUE DABG
3948543 130 0.00000
3063807 103 0.00000
3096575 183 0.00000
2949118 614 0.00000
3227645 369 0.00000
4014076 10 0.00000
2637819 4 0.04774
3850234 126 0.00000
3719161 242 0.00000
2916345 170 0.00000
2342904 79 0.00080
3817464 79 0.00000
2408437 104 0.04940
3932148 134 1.00000
3375091 466 0.00000
3653619 221 0.00000
2818035 10 0.00010
3063795 18 0.03635
2981874 75 0.00000
3227634 13 0.04850

Total number of rows: 17742

Table truncated, full table size 334 Kbytes.




Supplementary file Size Download File type/resource
GSM238540.cel.gz 22.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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