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Sample GSM325515 Query DataSets for GSM325515
Status Public on Dec 25, 2008
Title wt_206_GFP_neg3, biological replicate 3
Sample type RNA
 
Source name 206_GFP_neg
Organism Danio rerio
Characteristics non-muscle cells
wild-type zebrafish embryos, 16 hpf
Growth protocol Zebrafish embryos were incubated at 28C in the E3 soluion
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Affymetrix GeneArray Scanner.
Description Gene expression data from GFP-negative cells from the rest of the body
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
 
Submission date Sep 30, 2008
Last update date Nov 15, 2008
Contact name Alena Shkumatava
E-mail(s) shkumata@wi.mit.edu
Organization name Whitehead Institute/MIT
Department Bartel Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL1319
Series (1)
GSE12991 Isolation of single miRNA-expressing cells from zebrafish embryos

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 75.4 P 0.002867
AFFX-BioB-M_at 60.9 P 0.001248
AFFX-BioB-3_at 44.3 P 0.012547
AFFX-BioC-5_at 123.7 P 0.000127
AFFX-BioC-3_at 96.5 P 0.00011
AFFX-BioDn-5_at 368.5 P 0.000044
AFFX-BioDn-3_at 970.9 P 0.000147
AFFX-CreX-5_at 1947.2 P 0.000044
AFFX-CreX-3_at 2953.2 P 0.000044
AFFX-DapX-5_at 33.4 P 0.000857
AFFX-DapX-M_at 247.3 P 0.000972
AFFX-DapX-3_at 451.7 P 0.000044
AFFX-LysX-5_at 8.6 A 0.108979
AFFX-LysX-M_at 28.9 A 0.095667
AFFX-LysX-3_at 100.4 P 0.000081
AFFX-PheX-5_at 7.7 A 0.300606
AFFX-PheX-M_at 19.9 P 0.00844
AFFX-PheX-3_at 96 P 0.000169
AFFX-ThrX-5_at 12.6 A 0.41138
AFFX-ThrX-M_at 38 P 0.002867

Total number of rows: 15617

Table truncated, full table size 497 Kbytes.




Supplementary file Size Download File type/resource
GSM325515.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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