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Sample GSM94802 Query DataSets for GSM94802
Status Public on Apr 01, 2006
Title 15T
Sample type RNA
 
Channel 1
Source name Testicular DLBCL 15T
Organism Homo sapiens
Characteristics Tissue: Testicular diffuse large B cell lymphoma
Sample origin: whole frozen tissue sections
Sample type: RNA
Amplification: linear, one-round
Extracted molecule total RNA
Extraction protocol Total RNA was isolated and submitted to one round of linear amplification. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
Label Cy5 or Cy3 (dye-reversal)
Label protocol Cy3 or Cy5 molecules were directly incorporated during a cDNA synthesis reaction using amplified cRNA as starting material. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
 
Channel 2
Source name Reference tonsil mix
Organism Homo sapiens
Characteristics Tissue: 5 hyperplastic tonsils
Sample origin: whole frozen tissue sections
Sample type: RNA
Amplification: linear, one-round
Extracted molecule total RNA
Extraction protocol Total RNA was isolated and submitted to one round of linear amplification. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
Label Cy5 or Cy3 (dye-reversal)
Label protocol Cy3 or Cy5 molecules were directly incorporated during a cDNA synthesis reaction using amplified cRNA as starting material. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
 
 
Hybridization protocol Each hybridization was repeated as a dye reversal. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm
Scan protocol Fluorescent signals were extracted from the arrays by a DNA Microarray Scanner (Agilent, Palo Alto, California) and quantified using Imagene 5.5 software (Biodiscovery, El Segundo, California).
Description A mix of 5 hyperplastic tonsils was used as a common reference. Each hybridization was repeated as a dye-reversal.
Data processing Data were normalized and corrected for various biases according to Yang et al (PMID: 11842121). Ratios of expression in DLBCL (sample) compared to tonsil (reference) were calculated; weighted averages of dye-reversal experiments and confidence levels were calculated according to the Rosetta error model (Hughes et al, PMID: 10929718). Based on MA plots and the results from the error model, spots with an average intensity measurement A (0.5 log2 (Cy3Cy5)) lower than 7 over all experiments were excluded from further analysis.
 
Submission date Feb 01, 2006
Last update date Feb 27, 2006
Contact name Marije Booman
E-mail(s) m.booman@path.umcg.nl
Organization name University Medical Center Groningen
Department Pathology
Street address P.O. Box 30001
City Groningen
ZIP/Postal code 9700 RB
Country Netherlands
 
Platform ID GPL3408
Series (2)
GSE4157 Gene expression analysis of immune privileged site-associated DLBCL: The effect of HLA class II downregulation
GSE4296 Gene expression analysis of testicular DLBCL: ABC or GCB subtype?

Data table header descriptions
ID_REF
VALUE Log ratio (base 2) of sample/reference; normalized, weighted average of dye-reversal. Spots with an intensity A (0.5 log2 (Cy5Cy3)) lower than 7 over all samples are excluded from analysis (blank fields), leaving 14362 good quality spots.

Data table
ID_REF VALUE
1
2
3 0.01332534
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

Total number of rows: 19200

Table truncated, full table size 256 Kbytes.




Supplementary file Size Download File type/resource
GSM94802_ref_cy3.imagene.gz 921.5 Kb (ftp)(http) IMAGENE
GSM94802_ref_cy5.imagene.gz 910.3 Kb (ftp)(http) IMAGENE
GSM94802_sample_cy3.imagene.gz 927.9 Kb (ftp)(http) IMAGENE
GSM94802_sample_cy5.imagene.gz 918.0 Kb (ftp)(http) IMAGENE
Raw data provided as supplementary file

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