E-SMDB-2651 - Transcription profiling of 10 individual human cell lines to identify unique genes contributed by individual cell lines to UHRR

Status
Submitted on 1 November 2005, released on 1 November 2005, last updated on 4 June 2014
Organism
Homo sapiens
Samples (0)
Array (1)
Protocols (1)
Description
Total RNA isolated from 10 individual human cell lines were reverse-transcribed to cDNA, labeled with Cy5 and co-hybridized with Cy3-labeled UHRR onto 43,000-spot cDNA microarrays (Stanford University). The data was analyzed using GeneTraffic software. Approximately 6000-8000 spots out of 43,000 (14-18 %) were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics in only one cell line was determined.
Experiment types
transcription profiling by array, reference
Contacts
Citation
Universal Reference RNA as a standard for microarray experiments. Novoradovskaya N, Whitfield ML, Basehore LS, Novoradovsky A, Pesich R, Usary J, Karaca M, Wong WK, Aprelikova O, Fero M, Perou CM, Botstein D, Braman J. BMC Genomics 5(1):20 (2004), Europe PMC 15113400
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-SMDB-2651.idf.txt
Sample and data relationshipE-SMDB-2651.sdrf.txt
Raw data (1)E-SMDB-2651.raw.1.zip
Processed data (1)E-SMDB-2651.processed.1.zip
Array designA-SMDB-606.adf.txt
Links