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Sample GSM289391 Query DataSets for GSM289391
Status Public on May 19, 2008
Title rpL35 +/- MPNST_56
Sample type RNA
 
Source name Malignant peripheral nerve sheath tumors from fish heterozygous for inactivating mutation in ribosomal protein L35
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 6.182404237
Dr.10.1.S1_at 1.764166637
Dr.10.4.S1_a_at 2.567989606
Dr.100.1.A1_at 2.808919835
Dr.1000.1.S1_at 11.96199475
Dr.10000.1.A1_at 1.565518495
Dr.10005.1.A1_at 7.705032257
Dr.10006.1.A1_at 9.420771602
Dr.10010.1.A1_at 3.129770468
Dr.10011.1.A1_at 7.730973512
Dr.10012.1.A1_at 3.75135866
Dr.10014.1.A1_at 1.894512794
Dr.10015.1.S1_at 3.431192779
Dr.10015.2.S1_a_at 3.392680004
Dr.10015.2.S1_at 2.304314372
Dr.10016.1.A1_at 6.086891282
Dr.10018.1.S1_at 2.293219051
Dr.1002.1.S1_at 9.495533805
Dr.10022.1.S1_at 6.686479296
Dr.10023.1.A1_at 2.797464556

Total number of rows: 15502

Table truncated, full table size 433 Kbytes.




Supplementary file Size Download File type/resource
GSM289391.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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