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Sample GSM2645887 Query DataSets for GSM2645887
Status Public on Sep 06, 2017
Title MDAMB231_4175_sicontrol_1
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 5.253027472
ERCCmix1step10 4.498034
ERCCmix1step11 5.484881014
ERCCmix1step12 3.910232584
ERCCmix1step13 4.281440985
ERCCmix1step14 5.159359573
ERCCmix1step15 4.258338641
ERCCmix1step16 3.452670905
ERCCmix1step17 3.700920543
ERCCmix1step18 3.732627112
ERCCmix1step19 6.178696791
ERCCmix1step2 5.803519997
ERCCmix1step20 4.858404455
ERCCmix1step21 6.677468648
ERCCmix1step22 7.569878953
ERCCmix1step3 5.341846314
ERCCmix1step4 5.050075448
ERCCmix1step5 5.129891189
ERCCmix1step6 3.295822231
ERCCmix1step7 4.119051239

Total number of rows: 24320

Table truncated, full table size 729 Kbytes.

Supplementary file Size Download File type/resource
GSM2645887_211_JPS073-3_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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