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Sample GSM325521 Query DataSets for GSM325521
Status Public on Dec 25, 2008
Title wt_124_GFP_neg3, biological replicate 3
Sample type RNA
Source name 124_GFP_neg
Organism Danio rerio
Characteristics non-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-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
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
VALUE MAS5.0 signal intensity

Data table
AFFX-BioB-5_at 62.8 P 0.002556
AFFX-BioB-M_at 57.4 P 0.00141
AFFX-BioB-3_at 35.9 P 0.028457
AFFX-BioC-5_at 125.4 P 0.000127
AFFX-BioC-3_at 91.9 P 0.000081
AFFX-BioDn-5_at 354.8 P 0.000044
AFFX-BioDn-3_at 895.6 P 0.000195
AFFX-CreX-5_at 1784.3 P 0.000044
AFFX-CreX-3_at 2484.7 P 0.000052
AFFX-DapX-5_at 23.7 P 0.006187
AFFX-DapX-M_at 187.4 P 0.000857
AFFX-DapX-3_at 333.6 P 0.000052
AFFX-LysX-5_at 1.4 A 0.455413
AFFX-LysX-M_at 33.2 A 0.078002
AFFX-LysX-3_at 80.4 P 0.000044
AFFX-PheX-5_at 3.7 A 0.440646
AFFX-PheX-M_at 17.3 A 0.0727
AFFX-PheX-3_at 74 P 0.000147
AFFX-ThrX-5_at 16 A 0.262827
AFFX-ThrX-M_at 29 P 0.004998

Total number of rows: 15617

Table truncated, full table size 497 Kbytes.

Supplementary file Size Download File type/resource
GSM325521.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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