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Sample GSM1529769 Query DataSets for GSM1529769
Status Public on Mar 20, 2015
Title 152 primary tumor explant
Sample type RNA
 
Source name 152 primary tumor explant
Organism Mus musculus
Characteristics cell type: primary tumor 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 1.1828753
A_52_P580582 0.9673558
A_52_P403405 1.4955596
A_52_P819156 1.0700343
A_51_P331831 1.0080345
A_51_P430630 1.3867412
A_52_P502357 1.5486307
A_52_P299964 0.71891725
A_51_P356389 1.0471916
A_52_P684402 0.8907482
A_51_P414208 1
A_51_P280918 0.9200697
A_52_P613688 0.9231914
A_52_P258194 0.88313824
A_52_P229271 1.1385365
A_52_P214630 0.9741206
A_52_P579519 1.1425225
A_52_P979997 1.0280352
A_52_P453864 1.0029752
A_52_P655842 0.8193927

Total number of rows: 41265

Table truncated, full table size 906 Kbytes.




Supplementary file Size Download File type/resource
GSM1529769_152_primary_tumor_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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