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Sample GSM325527 Query DataSets for GSM325527
Status Public on Dec 25, 2008
Title MZ_124_GFP_neg3, biological replicate 3
Sample type RNA
 
Source name MZ_124_GFP_neg
Organism Danio rerio
Characteristics non-CNS cells
Mzdicer mutant zebrafish embryos, 14-16 somites
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 56.7 P 0.001248
AFFX-BioB-M_at 73.6 P 0.00007
AFFX-BioB-3_at 39.8 P 0.006871
AFFX-BioC-5_at 131.9 P 0.00006
AFFX-BioC-3_at 115 P 0.000052
AFFX-BioDn-5_at 439.7 P 0.000044
AFFX-BioDn-3_at 741.5 P 0.000044
AFFX-CreX-5_at 1943.4 P 0.000044
AFFX-CreX-3_at 3538.2 P 0.000044
AFFX-DapX-5_at 25.9 P 0.002275
AFFX-DapX-M_at 218.4 P 0.00007
AFFX-DapX-3_at 458.6 P 0.000044
AFFX-LysX-5_at 6.7 A 0.089478
AFFX-LysX-M_at 32.3 P 0.00762
AFFX-LysX-3_at 94 P 0.000044
AFFX-PheX-5_at 7 A 0.139482
AFFX-PheX-M_at 25.5 P 0.000258
AFFX-PheX-3_at 84.2 P 0.000127
AFFX-ThrX-5_at 14.6 A 0.102165
AFFX-ThrX-M_at 41.1 P 0.000258

Total number of rows: 15617

Table truncated, full table size 497 Kbytes.




Supplementary file Size Download File type/resource
GSM325527.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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