E-MTAB-298 - Transcription profiling by array of human chronic lymphocytic leukemia, colorectal cancer and normal samples to measure the transcription of pyknons loci

Status
Submitted on 13 July 2010, last updated on 3 May 2014, released on 14 July 2014
Organism
Homo sapiens
Samples (42)
Array (1)
Protocols (6)
Description
The transcription of pyknons loci was measured in several normal and malignant tissues including colorectal cancers and chronic lymphocytic leukemias. The levels of expression in malignant cells was compared to that of corresponding normals, the colon epithelium and the B lymphocytes, respectively. The expression of the sense and antisense transcripts in respect with the pyknon orientation was measured for 1179 pyknons. The arrays (MDACC v5 version) were imported into BRB Research Branch (BRB) array tools 3.8.1 (http://linus.nci.nih.gov/BRB-ArrayTools.html), average values of the replicate spots of each ncRNA were background subtracted, normalized, and subjected to further analysis. Normalization was performed by using per chip median normalization method and the median array as reference. Finally, we excluded a ncRNA if less than 20 % of expression data have at least a 1.5 -fold change in either direction from gene's median value. Absent calls were thresholded to 7 (log2) before statistical analysis. This level is the average minimum intensity level detected in the experiments.
Experiment types
transcription profiling by array, disease state
Contact
Citation
tbc.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-298.idf.txt
Sample and data relationshipE-MTAB-298.sdrf.txt
Raw data (1)E-MTAB-298.raw.1.zip
Processed data (1)E-MTAB-298.processed.1.zip
Array designA-MEXP-1738.adf.txt
Links