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Sample GSM2645910 Query DataSets for GSM2645910
Status Public on Sep 06, 2017
Title NMuMG-ErbB2/VC_PBS_1
Sample type RNA
 
Source name lung metastasis, control, PBS
Organism Mus musculus
Characteristics tissue: metastasis lung tissue
cell line: NMuMG-ErbB2/VC (control)
Treatment protocol lung were perfused with 50% optimal cutting temperature solution, diluted in PBS and removed and embedded in OCT at -80degC
Growth protocol lung metastasis from mice treated with phenformin or PBS was extracted by laser capture microdissection (LCM) from slides
Extracted molecule total RNA
Extraction protocol Lung metastasis RNA was isolated using LCM and pico RNA kit.
Label pico RNA kit
Label protocol Sense-strand cDNA was synthesized from 10 ng of total RNA and fragmentation and labeling were performed to produce ds DNA with the GeneChip® Pico Labeling Kit according to manufacturer’s instructions (Applied Biosystems)
 
Hybridization protocol After fragmentation and labeling, 4 µg DNA target was hybridized on GeneChip® Mouse Clariom™ S (ThermoFisher) and incubated at 450C in the Genechip® Hybridization oven 640 (ThermoFisher) for 17 hours at 60 rpm
Scan protocol The microarrays were finally scanned on a GeneChip® scanner 3000 (ThermoFisher).
Description expression data of lung metastatic tissue from mice injected with control cells, treated with PBS
Data processing Bioconductor Oligo R package. The file 'normalized_data_allcontrols.txt' contains data for all probe sets including controls. The sample table does not include data for AFFX controls or *RPTR controls.
 
Submission date Jun 01, 2017
Last update date Jan 23, 2018
Contact name Julie St-Pierre
E-mail(s) julie.st-pierre@mcgill.ca
Organization name McGill University
Department Department of Biochemistry
Street address 3655 Promenade Sir William Osler
City Montreal
State/province Quebec
ZIP/Postal code H3G 1Y6
Country Canada
 
Platform ID GPL23038
Series (2)
GSE99555 Expression data from lung metastasis
GSE99557 Expression data from a lung metastatic cell line or metastatic explants in mouse and human

Data table header descriptions
ID_REF
VALUE log2 GC-RMA signal

Data table
ID_REF VALUE
ERCCmix1step1 5.431618328
ERCCmix1step10 5.140097507
ERCCmix1step11 7.764608229
ERCCmix1step12 3.814417128
ERCCmix1step13 4.39400669
ERCCmix1step14 4.659346906
ERCCmix1step15 4.242253615
ERCCmix1step16 3.647925039
ERCCmix1step17 4.540098827
ERCCmix1step18 4.315847662
ERCCmix1step19 5.752841151
ERCCmix1step2 6.979322462
ERCCmix1step20 4.579912093
ERCCmix1step21 6.705531183
ERCCmix1step22 7.307536816
ERCCmix1step3 5.244200769
ERCCmix1step4 5.085308397
ERCCmix1step5 4.977679754
ERCCmix1step6 4.01881964
ERCCmix1step7 4.936593447

Total number of rows: 28815

Table truncated, full table size 860 Kbytes.




Supplementary file Size Download File type/resource
GSM2645910_44_JPS096C06C06_01.CEL.gz 1010.7 Kb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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