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Sample GSM289399 Query DataSets for GSM289399
Status Public on May 19, 2008
Title rpS11 +/- MPNST
Sample type RNA
 
Source name Malignant peripheral nerve sheath tumors from fish heterozygous for inactivating mutation in ribosomal protein S11
Organism Danio rerio
Characteristics Late stage MPNST from zebrafish fish 18-24 months old
Treatment protocol Tumors were dissected from zebrafish anaesthetized with 0.03% MESAB
Growth protocol Zebrafish raised according to standard protocols
Extracted molecule total RNA
Extraction protocol Trizol according to the manufacturer's protocol
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA according to the Affymetrix Expression Analysis Technical Manual.
 
Hybridization protocol Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Zebrafish Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (A4 samples) or 450 (A5 and A7 samples).
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (A4 samples) or Affymetrix 7G scanner (A5 and A7 samples).
Description no additional information
Data processing Bioconductor Affy package and gcRMA
 
Submission date May 19, 2008
Last update date May 19, 2008
Contact name Charles Arthur Whittaker
E-mail(s) charliew@mit.edu
Organization name Koch Institute
Street address 77 Mass Ave 76-189
City Cambridge
State/province MA
ZIP/Postal code 02152
Country USA
 
Platform ID GPL1319
Series (1)
GSE11493 Comparison of transcripts in zebrafish tumors

Data table header descriptions
ID_REF
VALUE gcRMA-calculated, log2 expression values

Data table
ID_REF VALUE
Dr.1.1.S1_at 6.674644498
Dr.10.1.S1_at 1.611069448
Dr.10.4.S1_a_at 2.189800735
Dr.100.1.A1_at 2.600812465
Dr.1000.1.S1_at 11.85007371
Dr.10000.1.A1_at 1.396189744
Dr.10005.1.A1_at 8.196733353
Dr.10006.1.A1_at 8.838835564
Dr.10010.1.A1_at 2.483081861
Dr.10011.1.A1_at 7.350218028
Dr.10012.1.A1_at 4.921252962
Dr.10014.1.A1_at 1.714931554
Dr.10015.1.S1_at 2.795629087
Dr.10015.2.S1_a_at 3.256710235
Dr.10015.2.S1_at 2.05024655
Dr.10016.1.A1_at 6.376223196
Dr.10018.1.S1_at 2.061686152
Dr.1002.1.S1_at 9.257942672
Dr.10022.1.S1_at 6.541651707
Dr.10023.1.A1_at 1.761801892

Total number of rows: 15502

Table truncated, full table size 433 Kbytes.




Supplementary file Size Download File type/resource
GSM289399.CEL.gz 3.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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