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Sample GSM289389 Query DataSets for GSM289389
Status Public on May 19, 2008
Title rpL35 +/- MPNST_54
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 5.51310281
Dr.10.1.S1_at 1.789551485
Dr.10.4.S1_a_at 2.398014451
Dr.100.1.A1_at 2.85540325
Dr.1000.1.S1_at 11.36987427
Dr.10000.1.A1_at 1.589519946
Dr.10005.1.A1_at 7.358474034
Dr.10006.1.A1_at 9.334063232
Dr.10010.1.A1_at 2.832817228
Dr.10011.1.A1_at 8.209365904
Dr.10012.1.A1_at 4.804609736
Dr.10014.1.A1_at 1.914760839
Dr.10015.1.S1_at 3.296704499
Dr.10015.2.S1_a_at 3.439740479
Dr.10015.2.S1_at 2.440388668
Dr.10016.1.A1_at 6.634112758
Dr.10018.1.S1_at 2.403552795
Dr.1002.1.S1_at 8.154756956
Dr.10022.1.S1_at 6.118880173
Dr.10023.1.A1_at 2.000686904

Total number of rows: 15502

Table truncated, full table size 433 Kbytes.




Supplementary file Size Download File type/resource
GSM289389.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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