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Sample GSM1529776 Query DataSets for GSM1529776
Status Public on Mar 20, 2015
Title 593 bone-aggressive explant
Sample type RNA
 
Source name 593 bone-aggressive explant
Organism Mus musculus
Characteristics cell type: bone-aggressive explant
Growth protocol All cell lines were grown in DMEM supplemented with 10% fetal bovine serum, 10 mmol/L HEPES, 1 mmol/L sodium pyruvate, 1.5 g/L sodium bicarbonate, penicillin/streptomycin, and fungizone.
Extracted molecule total RNA
Extraction protocol RNA was extracted from 4T1 parental and individual in vivo selected metastatic sub-populations using RNeasy Mini Kits and QIAshredder columns (Qiagen, Mississauga, ON, Canada).
Label cy5
Label protocol Purified total RNA (40 ng) was subjected to two consecutive rounds of T7-based amplification using Amino Allyl MessageAmp II kits (Applied Biosystems, Streetsville, ON, Canada) and the resulting aRNA was conjugated to Cy5 dyes (GE Healthcare Bio-sciences, Bair d’Urfe, QC, Canada).
 
Hybridization protocol Hybridization to 44K whole mouse genome microarray gene expression chips (Agilent Technologies) was conducted following manufacturer’s protocol (Agilent Technologies).
Scan protocol Microarray chips were then washed and immediately scanned using a DNA Microarray Scanner (Model G2565BA, Agilent Technologies).
Data processing Microarray data were feature extracted using Feature Extraction Software (v. 9.5.3.1) available from Agilent, using the default variables. Microarray expression data were normalized and analyzed using GeneSpring software (V7.3, Agilent Technologies). Each group (parental cell line and the explants derived form mammary fat pad, bone, lung and liver metastasis) was individually compared to all the other groups. A two-fold change cut off was determined and differentially expressed genes were selected using a non-parametric test coupled with a false discovery rate of 0.05.
 
Submission date Oct 22, 2014
Last update date Mar 20, 2015
Contact name Peter M Siegel
Organization name McGill University
Department Medicine
Lab Room 513
Street address 1160 Pine avenue West
City Montreal
State/province Quebec
ZIP/Postal code H3A 1A3
Country Canada
 
Platform ID GPL7202
Series (1)
GSE62598 Granulocytic immune infiltrates are essential for the efficient formation of breast cancer liver metastases

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_52_P616356 1.4242588
A_52_P580582 0.8023221
A_52_P403405 2.0795865
A_52_P819156 0.9614558
A_51_P331831 1.4212648
A_51_P430630 0.40493077
A_52_P502357 0.79238397
A_52_P299964 0.535583
A_51_P356389 1.9161718
A_52_P684402 0.9863651
A_51_P414208 0.2893873
A_51_P280918 0.8875359
A_52_P613688 1
A_52_P258194 0.7190397
A_52_P229271 1.1878146
A_52_P214630 0.83738846
A_52_P579519 1.07763
A_52_P979997 1.5903924
A_52_P453864 1.2419477
A_52_P655842 1.0319408

Total number of rows: 41265

Table truncated, full table size 913 Kbytes.




Supplementary file Size Download File type/resource
GSM1529776_593_bone-aggressive_explant.txt.gz 16.1 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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