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Sample GSM371279 Query DataSets for GSM371279
Status Public on Feb 13, 2010
Title MDCK-Early Passage-biological replicate1
Sample type RNA
 
Source name Total RNA from early passage MDCK were plated on tissue culture flasks and allowed to polarize for four days
Organism Canis lupus familiaris
Characteristics species: Canine
gender: Female
organ: Kidney
cell line: Madin Darby Canine Kidney
Biomaterial provider Total RNA was received from Erik Young at the Department of Surgery, Hackensack University Medical Center, Hackensack, NJ
Treatment protocol Early and late passage MDCK from T25 flasks that had been seeded with 8 x 105 cells and allowed to become confluent and polarize over 4 days in culture cells
Growth protocol MDCK cells were obtained from the ATCC at passage number 55 (CCL-34) and were subcultured in MEM (ATCC) supplemented with 10% fetal bovine serum (Sigma) and an antibiotic/antimycotic (Invitrogen). Cells were cultured for 4-7 days before being re-seeded at 4-12 x 103 cells/cm2 in T25 culture flasks. Cells were maintained in humidified incubator at 37oC and 5% CO2 and were fed three times per week.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from biological triplicates of early and late passage MDCK from T25 flasks using a Ribopure kit (Ambion, Austin, TX). Acquired RNA was precipitated with EtOH and subsequently purified employing columns, procedures and reagents from an RNEasy kit (Qiagen, Germantown, MD) and resuspended in RNAse-free H2O provided.
Label Biotin
Label protocol Complementary DNA and complemetary RNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in-vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY).
 
Hybridization protocol Fifteen micrograms of cRNA was fragmented for hybridization to Affymetrix Canine Genome 2.0 Array GeneChips (Santa Clara, CA), which contains approximately 18,000 C. familiaris mRNA/EST-based transcripts and over 20,000 non-redundant predicted genes. Hybridization was done overnight at 45°C for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed with the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4_450 protocol
Scan protocol Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
Description Young_E1_08-01-07
Data processing Expression intensity values were extracted from the raw image files using the Robust Multi-Array Average algorithm with the Affymetrix Expression ConsoleTM. Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set
 
Submission date Feb 13, 2009
Last update date Feb 17, 2009
Contact name Saleena Ghanny
E-mail(s) ghannysa@njms.rutgers.edu
Organization name Rutgers University
Street address 185 South Orange Ave
City Newark
ZIP/Postal code 07103
Country USA
 
Platform ID GPL3738
Series (1)
GSE14837 Madin Darby Canine Kidney (MDCK) Cells: Early & Late Passage

Data table header descriptions
ID_REF
VALUE RMA processed values

Data table
ID_REF VALUE
AFFX-BioB-5_at 7.67468
AFFX-BioB-M_at 8.14842
AFFX-BioB-3_at 7.72258
AFFX-BioC-5_at 7.65057
AFFX-BioC-3_at 7.52264
AFFX-BioDn-5_at 10.2944
AFFX-BioDn-3_at 11.9382
AFFX-CreX-5_at 12.8865
AFFX-CreX-3_at 13.2749
AFFX-DapX-5_at 4.35323
AFFX-DapX-M_at 4.49203
AFFX-DapX-3_at 4.54251
AFFX-LysX-5_at 4.30405
AFFX-LysX-M_at 4.54695
AFFX-LysX-3_at 4.32207
AFFX-PheX-5_at 4.33264
AFFX-PheX-M_at 4.39035
AFFX-PheX-3_at 5.99336
AFFX-ThrX-5_at 4.71821
AFFX-ThrX-M_at 4.37332

Total number of rows: 43035

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM371279.CEL.gz 3.8 Mb (ftp)(http) CEL
GSM371279.chp.gz 335.6 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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