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Sample GSM325513 Query DataSets for GSM325513
Status Public on Dec 25, 2008
Title wt_206_GFP_neg2, biological replicate 2
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 92.3 P 0.002556
AFFX-BioB-M_at 86.6 P 0.001248
AFFX-BioB-3_at 48.5 P 0.00844
AFFX-BioC-5_at 146.2 P 0.000297
AFFX-BioC-3_at 148 P 0.000052
AFFX-BioDn-5_at 528.6 P 0.000044
AFFX-BioDn-3_at 1199.7 P 0.000169
AFFX-CreX-5_at 2520.2 P 0.000044
AFFX-CreX-3_at 3497.9 P 0.000052
AFFX-DapX-5_at 31.3 P 0.005565
AFFX-DapX-M_at 262 P 0.000972
AFFX-DapX-3_at 544.1 P 0.000052
AFFX-LysX-5_at 9.5 A 0.185131
AFFX-LysX-M_at 27.2 A 0.0727
AFFX-LysX-3_at 126.4 P 0.00007
AFFX-PheX-5_at 9.7 A 0.195266
AFFX-PheX-M_at 17.4 P 0.002275
AFFX-PheX-3_at 106.7 P 0.00034
AFFX-ThrX-5_at 25.5 A 0.175328
AFFX-ThrX-M_at 50.6 P 0.00141

Total number of rows: 15617

Table truncated, full table size 497 Kbytes.




Supplementary file Size Download File type/resource
GSM325513.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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