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Sample GSM289397 Query DataSets for GSM289397
Status Public on May 19, 2008
Title rpL14 +/- MPNST
Sample type RNA
 
Source name Malignant peripheral nerve sheath tumors from fish heterozygous for inactivating mutation in ribosomal protein L14
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 5.392105946
Dr.10.1.S1_at 1.607950458
Dr.10.4.S1_a_at 2.185805316
Dr.100.1.A1_at 2.459689637
Dr.1000.1.S1_at 11.9545713
Dr.10000.1.A1_at 1.370277878
Dr.10005.1.A1_at 7.561856824
Dr.10006.1.A1_at 8.89431031
Dr.10010.1.A1_at 2.272956667
Dr.10011.1.A1_at 8.41861706
Dr.10012.1.A1_at 4.699730503
Dr.10014.1.A1_at 1.679714462
Dr.10015.1.S1_at 2.787430238
Dr.10015.2.S1_a_at 3.229943139
Dr.10015.2.S1_at 1.972463493
Dr.10016.1.A1_at 6.391214467
Dr.10018.1.S1_at 2.022201005
Dr.1002.1.S1_at 8.735777387
Dr.10022.1.S1_at 6.213489225
Dr.10023.1.A1_at 1.71387413

Total number of rows: 15502

Table truncated, full table size 433 Kbytes.




Supplementary file Size Download File type/resource
GSM289397.CEL.gz 3.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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