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Sample GSM1498281 Query DataSets for GSM1498281
Status Public on Sep 12, 2014
Title Py15-4T2
Sample type RNA
 
Source name Py15-4 cell line tumor
Organism Mus musculus
Characteristics tumor type: C57BL/6 PyVmT cell line derived tumor
tumor phenotype/subtype: Claudin low
Extracted molecule total RNA
Extraction protocol tumor collection protocol: Spontaneous C57Bl/6 PyVmT tumors 0.8-1cm in diameter were dissected and stored frozen at -80°C until RNA isolation procedures.
tumor collection protocol: Tumor cells from various C57Bl/6 PyVmT-derived clonal cell lines were injected at 10^6 cells in 2 mg/ml matrigel into the abdominal mammary fat pads of female C57Bl/6 mice. At 6-8 weeks, tumors 0.8-1cm in diameter were dissected and stored frozen at -80°C until RNA isolation procedures. In some cases tumors were enzymatically digested and cell suspensions reinjected into the mammary fat pads of new syngeneic recipients.
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the UCSD (University of California, San Diego, La Jolla, CA, USA).
Label Cy3
Label protocol Labeling was performed by the VA/VMRF Microarray and NGS Core Facility at UCSD following the NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by the VA/VMRF Microarray and NGS Core Facility at UCSD following the NimbleGen Systems Inc., Madison, WI, USA standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by the VA/VMRF Microarray and NGS Core Facility at UCSD following the NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.
Description LE41
This sample is of a Py15-4 cell line-derived mammary tumor. Py15-4 was derived from the Py230 cell line. It is the second tumor used in this experiment, each from independent animals.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Sep 04, 2014
Last update date Sep 12, 2014
Contact name Lesley G Ellies
E-mail(s) lellies@ucsd.edu
Phone 858-822-4167
Organization name University of California, San Diego
Department Pathology
Street address 9500 Gilman Drive
City La Jolla
State/province California
ZIP/Postal code 92093
Country USA
 
Platform ID GPL15887
Series (1)
GSE61138 Multipotent mammary cancer stem cells integrate stem cell and clonal expansion theories of tumor progression

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AB000096 307.511
AB000490 66.286
AB001425 1284.766
AB001435 113.462
AB001539 4014.313
AB001750 3667.073
AB001926 7757.558
AB003502 10921.912
AB004048 1474.208
AB005662 3673.713
AB005665 68.451
AB005909 28.961
AB006034 33.961
AB006103 24.561
AB007407 111.76
AB008928 105.716
AB009369 74.462
AB010088 29.209
AB010122 11498.684
AB011499 6082.824

Total number of rows: 44170

Table truncated, full table size 745 Kbytes.




Supplementary file Size Download File type/resource
GSM1498281_471026A05_LE41_10527_Ellies_532.tif_gridded.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table

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