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Sample GSM2645888 Query DataSets for GSM2645888
Status Public on Sep 06, 2017
Title MDAMB231_4175_sicontrol_2
Sample type RNA
Source name 4175 cells, sicontrol
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 sicontrol
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 5.460370531
ERCCmix1step10 4.608341944
ERCCmix1step11 5.42593886
ERCCmix1step12 3.951067207
ERCCmix1step13 4.283661875
ERCCmix1step14 5.19311104
ERCCmix1step15 4.105197541
ERCCmix1step16 3.431259848
ERCCmix1step17 3.59522809
ERCCmix1step18 3.755376767
ERCCmix1step19 6.024529478
ERCCmix1step2 6.023485525
ERCCmix1step20 4.796835576
ERCCmix1step21 6.860881996
ERCCmix1step22 7.511450344
ERCCmix1step3 5.327376367
ERCCmix1step4 4.960630259
ERCCmix1step5 5.11414048
ERCCmix1step6 3.191749166
ERCCmix1step7 4.397180183

Total number of rows: 24320

Table truncated, full table size 729 Kbytes.

Supplementary file Size Download File type/resource
GSM2645888_212_JPS074-3_01.CEL.gz 1.2 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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