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Sample GSM1529765 Query DataSets for GSM1529765
Status Public on Mar 20, 2015
Title 4T1 parental rep D
Sample type RNA
 
Source name 4T1 parental rep D
Organism Mus musculus
Characteristics cell line: 4T1 parental
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 0.86124754
A_52_P580582 0.9896817
A_52_P403405 0.77357835
A_52_P819156 1.0380986
A_51_P331831 1.1950687
A_51_P430630 0.8682029
A_52_P502357 0.5351819
A_52_P299964 1.0489731
A_51_P356389 1.4508703
A_52_P684402 0.90482146
A_51_P414208 0.32194623
A_51_P280918 0.9059107
A_52_P613688 1.6276339
A_52_P258194 1.2432266
A_52_P229271 1.29284
A_52_P214630 1
A_52_P579519 0.7827684
A_52_P979997 0.7531833
A_52_P453864 0.7338031
A_52_P655842 1

Total number of rows: 41265

Table truncated, full table size 913 Kbytes.




Supplementary file Size Download File type/resource
GSM1529765_4T1_parental_D.txt.gz 15.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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