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Sample GSM2645912 Query DataSets for GSM2645912
Status Public on Sep 06, 2017
Title NMuMG-ErbB2/VC_PBS_3
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 5.270832785
ERCCmix1step10 4.646423137
ERCCmix1step11 7.022389476
ERCCmix1step12 3.561501222
ERCCmix1step13 4.065147598
ERCCmix1step14 4.666539293
ERCCmix1step15 4.118726102
ERCCmix1step16 3.431537191
ERCCmix1step17 4.130056091
ERCCmix1step18 4.212696751
ERCCmix1step19 5.736583423
ERCCmix1step2 6.714587753
ERCCmix1step20 4.162971885
ERCCmix1step21 6.194610337
ERCCmix1step22 7.475971117
ERCCmix1step3 5.002005773
ERCCmix1step4 4.858336488
ERCCmix1step5 4.874046786
ERCCmix1step6 3.265750614
ERCCmix1step7 4.985666264

Total number of rows: 28815

Table truncated, full table size 860 Kbytes.




Supplementary file Size Download File type/resource
GSM2645912_47_JPS098C08C08_01.CEL.gz 1.1 Mb (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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