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Sample GSM2645913 Query DataSets for GSM2645913
Status Public on Sep 06, 2017
Title NMuMG-ErbB2/VC_PBS_4
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 5.020933309
ERCCmix1step10 4.666887849
ERCCmix1step11 7.091009043
ERCCmix1step12 3.688904859
ERCCmix1step13 3.70935503
ERCCmix1step14 4.639291288
ERCCmix1step15 4.423409712
ERCCmix1step16 3.335512371
ERCCmix1step17 4.296484842
ERCCmix1step18 4.487269935
ERCCmix1step19 5.556837378
ERCCmix1step2 6.885578466
ERCCmix1step20 4.096310662
ERCCmix1step21 6.129291638
ERCCmix1step22 7.415984544
ERCCmix1step3 5.322507055
ERCCmix1step4 5.08908622
ERCCmix1step5 4.931417485
ERCCmix1step6 3.316834692
ERCCmix1step7 4.844585672

Total number of rows: 28815

Table truncated, full table size 861 Kbytes.




Supplementary file Size Download File type/resource
GSM2645913_48_JPS099C09C09_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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