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Sample GSM846209 Query DataSets for GSM846209
Status Public on Jan 01, 2015
Title M3 tumor dnTbRII, biological rep2
Sample type RNA
 
Source name MCF10CA1h (M3) tumor, TGF-beta pathway blockade with dnTbRII
Organism Homo sapiens
Characteristics tissue: Breast cancer xenograft tumor
treatment: TGF-beta pathway blockade with dnTbRII
Treatment protocol refer to the summary for each study.
Growth protocol MCF10CA1h (M3) cells were infected ex vivo with pLPCX retrovirus with no insert (M3-CON) or pLPCX expressing dominant negative type II TGF-b receptor (M3-dnTbRII) . Cells were selected in DMEM/F12 medium supplemented with 5% Horse serum and 4ug/ml puromycin for 5 days. 5x10e5 cells were implanted orthotopically into female athymic NCr nu/nu mice.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted and purified by RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).
Label Biotin
Label protocol 100 ng of RNA was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol. Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.
 
Hybridization protocol Three replicates of each group were hybridized to Affymetrix mouse (human) Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs. Wash and stain were performed on Affymetrix Fluidics Station 450
Scan protocol Genechips were scanned using an Affymetrix GeneChip Scanner 3000 and data was collected using Affymetrix AGCC software.
Description RNA extracted by Rneasy
Data processing Data were analyzed with Partek Genomics Suite (version 6.5) software using the RMA normalization algorithm with default format. More details needed here?
Original, Summarized, Difference, Filename, Chip Type, tumor, Scan Date, gene expression
 
Submission date Dec 08, 2011
Last update date Jan 01, 2015
Contact name Howard Yang
E-mail(s) yanghow@mail.nih.gov
Phone 2402765257
Organization name NCI
Street address 9609 Medical Center Dr.
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 
Platform ID GPL10739
Series (2)
GSE34276 Global analysis of TGF-beta-regulated gene expression in MCF10Ca1h (M3) breast tumor xenografts
GSE34277 MCF10A-based xenograft model of breast cancer

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
7896737 3.59692
7896739 2.67447
7896741 3.02552
7896743 4.95048
7896745 4.80558
7896747 7.88989
7896749 7.69263
7896751 2.49931
7896753 7.81418
7896755 5.31793
7896757 4.17837
7896758 4.3744
7896760 4.87171
7896762 11.0138
7896763 4.41035
7896764 4.99367
7896765 2.42906
7896766 5.92965
7896767 4.21213
7896768 9.173

Total number of rows: 253002

Table truncated, full table size 3926 Kbytes.




Supplementary file Size Download File type/resource
GSM846209_T_M3_dnTbRII_2.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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