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Sample GSM2645890 Query DataSets for GSM2645890
Status Public on Sep 06, 2017
Title MDAMB231_4175_siPGC1alpha_1
Sample type RNA
Source name 4175 cells, siPGC1alpha
Organism Homo sapiens
Characteristics cell line: MDA-MB-231 lung variant (4175)
Treatment protocol 4175 cells were treated with sicontrol or sipgc1alpha as described here, materials and methods
Growth protocol 4175 cells were cultured and grown as described in this paper, materials and methods
Extracted molecule total RNA
Extraction protocol RNA from 4175 cells were isolated in tissue culture using an Aurum Total RNA Mini Kit.
Label Aurum Total RNA Mini 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® Human 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 cell culture
expression data from human lung metastatic 4175 cells treated with siPGC1alpha
Data processing Bioconductor. The file 'normalized_data_allcontrols.txt' contains data for all probe sets including controls. The sample table does not include data for AFFX controls, *RPTR controls or probe sets named with 230*.
Submission date Jun 01, 2017
Last update date Jan 23, 2018
Contact name Julie St-Pierre
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 GPL23159
Series (2)
GSE99554 Expression data from a human lung metastatic cell line treated with siPGC1alpha or siControl
GSE99557 Expression data from a lung metastatic cell line or metastatic explants in mouse and human

Data table header descriptions
VALUE log2 GC-RMA signal

Data table
ERCCmix1step1 6.819277395
ERCCmix1step10 6.501884255
ERCCmix1step11 6.959520132
ERCCmix1step12 5.214658534
ERCCmix1step13 5.535301242
ERCCmix1step14 6.554621942
ERCCmix1step15 5.934639245
ERCCmix1step16 3.612387817
ERCCmix1step17 5.101779447
ERCCmix1step18 5.3817656
ERCCmix1step19 7.843137003
ERCCmix1step2 7.227364217
ERCCmix1step20 6.106243657
ERCCmix1step21 8.417602602
ERCCmix1step22 9.27798354
ERCCmix1step3 6.99818713
ERCCmix1step4 6.307260018
ERCCmix1step5 6.869697703
ERCCmix1step6 3.950735563
ERCCmix1step7 5.817104046

Total number of rows: 24320

Table truncated, full table size 730 Kbytes.

Supplementary file Size Download File type/resource
GSM2645890_214_JPS076-3_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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