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Sample GSM325516 Query DataSets for GSM325516
Status Public on Dec 25, 2008
Title wt_124_GFP_pos1, biological replicate 1
Sample type RNA
 
Source name 124_GFP_pos
Organism Danio rerio
Characteristics CNS 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-positive CNS cells
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 89.4 P 0.002275
AFFX-BioB-M_at 88.1 P 0.002867
AFFX-BioB-3_at 48.4 P 0.023929
AFFX-BioC-5_at 138.9 P 0.000095
AFFX-BioC-3_at 117.6 P 0.000052
AFFX-BioDn-5_at 405.9 P 0.000044
AFFX-BioDn-3_at 1115 P 0.000147
AFFX-CreX-5_at 2084.8 P 0.000044
AFFX-CreX-3_at 3459.4 P 0.000052
AFFX-DapX-5_at 32.2 P 0.005565
AFFX-DapX-M_at 155.9 P 0.001102
AFFX-DapX-3_at 292.2 P 0.00007
AFFX-LysX-5_at 4.4 A 0.440646
AFFX-LysX-M_at 18.8 A 0.250796
AFFX-LysX-3_at 83.4 P 0.00034
AFFX-PheX-5_at 1.7 A 0.760937
AFFX-PheX-M_at 18.7 A 0.078002
AFFX-PheX-3_at 80.2 P 0.002275
AFFX-ThrX-5_at 17 A 0.354453
AFFX-ThrX-M_at 28 P 0.018281

Total number of rows: 15617

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM325516.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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