NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1529771 Query DataSets for GSM1529771
Status Public on Mar 20, 2015
Title 526 lung-aggressive explant
Sample type RNA
 
Source name 526 lung-aggressive explant
Organism Mus musculus
Characteristics cell type: lung-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 0.7897391
A_52_P580582 0.8082258
A_52_P403405 1
A_52_P819156 0.7151158
A_51_P331831 0.7857069
A_51_P430630 0.92915565
A_52_P502357 2.01825
A_52_P299964 0.8294112
A_51_P356389 0.7323006
A_52_P684402 1.0428855
A_51_P414208 0.6709877
A_51_P280918 1.000637
A_52_P613688 0.52310634
A_52_P258194 0.582246
A_52_P229271 1
A_52_P214630 1.1777691
A_52_P579519 1.1396817
A_52_P979997 0.559312
A_52_P453864 0.21676466
A_52_P655842 0.38151678

Total number of rows: 41265

Table truncated, full table size 911 Kbytes.




Supplementary file Size Download File type/resource
GSM1529771_526_lung-aggressive_explant.txt.gz 16.1 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap