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Sample GSM546941 Query DataSets for GSM546941
Status Public on May 29, 2010
Title 4T07 biological replicate 1 (gene)
Sample type RNA
 
Source name 4T07
Organism Mus musculus
Characteristics cell line: 4T07
Treatment protocol Four mice were injected (1×10^-5 cells) with 168FARN, five mice with 4T07 and four mice with 4T01. Tumor volumes were calculated using the following formula: (?LW^2)/6, where L is the length and W is the width of the tumor. Tumors were surgically removed, using a cautery unit, once they reached a volume between 100 and 125 mm^3.
Growth protocol All cell lines were grown in DMEM supplemented with 10% fetal bovine serum, 10 mmol/L HEPES, 1 mmol/L sodium pyruvate, 1.5 g/L sodium bicarbonate, penicillin/streptomycin, and fungizone.
Extracted molecule total RNA
Extraction protocol Total RNA was purified using RNeasy Mini Kit Columns following the manufacturers instructions. We assessed The RNA quality using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). Tumors were hybridized independently at the functional genomics facility of McGill University and Genome Quebec Innovation Centre (Montreal, Quebec, Canada).
Label Biotin
Label protocol Biotin-labelled target for the microarray experiment were prepared using 1µg 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 Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip® Human Exon 1.0 ST array (Affymetrix) at 45˚C for 16-20 hours. Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed 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).
Description gene expression array
Data processing The Affymetrix Power Tools software package (Affymetrix) was used to quantile normalize the probe fluorescence intensities and to summarize the probe set (representing exon expression) and meta-probe set (representing gene expression) intensities. Transcript assignments were based on mm8 build. The library files for gene expression and exon expression are MoEx-1_0-st-v1.r2.dt1.mm8.core.mps.mask and MoEx-1_0-st-v1.r2.dt1.mm8.full.ps, respectively. Probeset intensities (exon data) : Probe logarithmic intensity error model (PLIER) for probe set intensities. The probeset_dabg.txt file on the Series record: Detection Above BackGround (DABG) statistics for probe set presence/absence. The meta probeset intensities (gene data): Iterative Probe logarithmic intensity error (ITER-PLIER) for meta-probe set intensities.
 
Submission date May 25, 2010
Last update date May 28, 2010
Contact name Amandine Bemmo
Organization name McGill University
Department Human Genetics
Lab McGill University and Genome Quebec Innovation Center
Street address 740, Dr Penfield Avenue
City Montréal
State/province Québec
ZIP/Postal code H3A 1A4
Country Canada
 
Platform ID GPL6096
Series (1)
GSE21994 Exon-level transcriptome profiling in murine breast cancer reveals splicing changes specific to tumors with different metastatic abilities
Relations
Alternative to GSM546970 (exon-level)

Data table header descriptions
ID_REF
VALUE Iterative Probe logarithmic intensity error (ITER-PLIER)

Data table
ID_REF VALUE
6848511 476.59976358669615592589252628386020660400390625000000
6864895 734.66922028983344716834835708141326904296875000000000
6766590 0.01159736670299721557342298439152727951295673847198
6914045 63.08556205542193850988041958771646022796630859375000
6963197 91.26246122054622844643745338544249534606933593750000
6766588 34.90327655453346977765249903313815593719482421875000
6995964 1197.13239734474723263701889663934707641601562500000000
6766587 16.55957068031476708824811794329434633255004882812500
6815739 74.88840983455254729506123112514615058898925781250000
6766586 114.91693049567251705411763396114110946655273437500000
7012346 32.43891831684585014272670377977192401885986328125000
6766585 65.37959224327792639996914658695459365844726562500000
6848505 1855.91995240190431104565504938364028930664062500000000
6766584 33.08277942547101702075451612472534179687500000000000
6848504 1370.15494514701867956318892538547515869140625000000000
6979576 78.19085473114623141555057372897863388061523437500000
6995960 205.56825271908755325966922100633382797241210937500000
6766583 23.48173225688938714483811054378747940063476562500000
6963191 34.60499661103814617035823175683617591857910156250000
6979575 2.23114250607998698683331895153969526290893554687500

Total number of rows: 16661

Table truncated, full table size 1023 Kbytes.




Supplementary file Size Download File type/resource
GSM546941_SR080529MEX02.CEL.gz 38.4 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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