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Sample GSM289398 Query DataSets for GSM289398
Status Public on May 19, 2008
Title rpS5 +/- MPNST
Sample type RNA
 
Source name Malignant peripheral nerve sheath tumors from fish heterozygous for inactivating mutation in ribosomal protein S5
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 8.176946007
Dr.10.1.S1_at 1.587271797
Dr.10.4.S1_a_at 2.172211884
Dr.100.1.A1_at 2.545024758
Dr.1000.1.S1_at 11.37971654
Dr.10000.1.A1_at 1.352943822
Dr.10005.1.A1_at 7.959819234
Dr.10006.1.A1_at 9.305046813
Dr.10010.1.A1_at 2.357418026
Dr.10011.1.A1_at 6.916405453
Dr.10012.1.A1_at 3.887621718
Dr.10014.1.A1_at 1.651152484
Dr.10015.1.S1_at 2.780574512
Dr.10015.2.S1_a_at 3.227343787
Dr.10015.2.S1_at 2.053649552
Dr.10016.1.A1_at 6.55464487
Dr.10018.1.S1_at 2.009961238
Dr.1002.1.S1_at 9.13277286
Dr.10022.1.S1_at 6.490176306
Dr.10023.1.A1_at 1.728720245

Total number of rows: 15502

Table truncated, full table size 433 Kbytes.




Supplementary file Size Download File type/resource
GSM289398.CEL.gz 3.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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