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Sample GSM517894 Query DataSets for GSM517894
Status Public on May 09, 2011
Title 3325K6A_TVA
Sample type RNA
 
Source name mouse mammary tumor, K6-tva RCAS-PyMT model
Organism Mus musculus
Characteristics background: FVB/N
tissue: mammary tumor
transgenic: K6-tva RCAS-PyMT
Growth protocol The K6-tva BAC transgenic line was generating using the recombineering method. Briefly, the RP23-473O22 BAC clone (200-kb) containing the K6a gene was purchased from BACPAC Resources Center (Children’s Hospital Oakland Research Institute, Oakland, California). The Counter Selection BAC Modification Kit (Gene Bridges GmbH, Dresden, Germany) was used to modify the BAC following the manufacturer’s instructions. All mice were on the FVB/N background, and were kept on 2920X Teklad Global Extruded Rodent Diet (Soy Protein-Free) (Harlan Laboratories, Indianapolis, Indiana). All procedures using mice were performed in compliance with an Institutional Animal Care and Use Committee-approved animal protocol.
Extracted molecule total RNA
Extraction protocol All samples were collected fresh and snap-frozen in liquid nitrogen. Frozen samples were ground into fine powder in liquid nitrogen and RNA was extracted by Trizol (Lift Technologies) with an additional step of the isopropanol precipitation following the regular isopropanol precipitation step recommended in the protocol. This extra step cleans up the potential chemical contamination in the Trizol reagents.
Label biotin
Label protocol Double-strand cDNA was synthesized from 5 µg of total RNA for each sample, and an in vitro transcription reaction was carried out to produce biotin-labeled cRNA from the cDNA. One-cycle target labeling and control reagents kit from Affymetrix (Part #900493) (Santa Clara, CA, USA) was used for the cDNA synthesis and biotin-labeling.
 
Hybridization protocol Total of 15 µg biotin-labeled cRNA was fragmented, and 10 µg of the fragmented cRNA was prepared in the hybridization cocktail in a total volume of 200 µl, and 6.5 µg of them in 130 µl volume was hybridized onto the M430A 2.0 GeneChip in an Affymetrix Hybridization Oven 640 for 16-19 hours. We used Affymetrix recommended procedures for prehybridization, hybridization, washing, and staining with streptavidin-phycoerythrin (SAPE). Antibody amplification was employed with a biotin-linked antibody to streptavidin (Vector Laboratories, Burlingame, CA).
Scan protocol After automated staining and washing (Affymetrix protocol Midi_euk2v3 450) using the GeneChip Fluidics Station 450, the arrays were scanned by the Affymetrix GeneChip scanner 3000 using the GeneChip operating system (GCOS) v1.2.
Description Mouse mammary tumor, K6-tva RCAS-PyMT model.
YL6-H33__3325K6A_TVA_PyMT_MG_430A_2.0
Data processing A low level quantification was done in the GCOS1.2, and the probe level data (CEL file) was saved for each array and analyzed subsequently by DNA chip analyzer (dChip v2006).
 
Submission date Mar 03, 2010
Last update date May 09, 2011
Contact name Chad Creighton
E-mail(s) [email protected]
Organization name Baylor College of Medicine
Department Biostatistics, Ducan Cancer Center
Street address One Baylor Plaza, Mail Stop: BCM305
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL8321
Series (1)
GSE20614 Gene expression profiling of mouse tumors arising from Keratin 6-positive mammary cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1415670_at 566.81
1415671_at 690.194
1415672_at 1404.768
1415673_at 222.969
1415674_a_at 323.874
1415675_at 216.676
1415676_a_at 1320.231
1415677_at 304.769
1415678_at 436.972
1415679_at 1242.905
1415680_at 606.606
1415681_at 434.721
1415682_at 140.805
1415683_at 1434.302
1415684_at 285.951
1415685_at 294.14
1415686_at 885.43
1415687_a_at 3822.123
1415688_at 1049.518
1415689_s_at 147.769

Total number of rows: 22690

Table truncated, full table size 420 Kbytes.




Supplementary file Size Download File type/resource
GSM517894.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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