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Sample GSM206403 Query DataSets for GSM206403
Status Public on Jan 01, 2008
Title Uninfected_rep2_10754
Sample type RNA
Source name Whole 6dpf uninfected zebrafish larvae
Organism Danio rerio
Characteristics Strain: AB, Age: 6 days post-fertilization (6dpf), Tissue: whole larvae, Rearing conditions: conventional, Microbial status: uninfected, Replicate: 2 of 3
Extracted molecule total RNA
Extraction protocol Total RNA was purified from pooled intact zebrafish larvae (31-82 larvae/pool, 3 biological replicate pools/condition) using Trizol reagent (Invitrogen) followed by DNase I digestion (DNA-Free, Ambion) according to manufacturers' protocols.
Label biotin
Label protocol Total RNA from each replicate pool (12ug RNA/replicate) was used as template for independent cDNA synthesis and in vitro transcription reactions (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) to generate biotinylated cRNA targets. cRNA targets (30ug/replicate) were fragmented using standard methods. For detailed protocols, see
Hybridization protocol Hybridization performed using standard Affymetrix protocol available at
Scan protocol Scanning performed using standard Affymetrix protocol available at
Description Whole 6dpf uninfected zebrafish larvae
Data processing Raw expression values were normalized (Invariant set method) and modelled (PM-MM model), and present/absent calls were generated using dChip software (build date Dec.11, 2005).
Submission date Jun 28, 2007
Last update date Aug 14, 2011
Contact name John F Rawls
Phone 919-966-8340
Fax 919 966-6927
Organization name University of North Carolina at Chapel Hill
Department Department of Cell and Molecular Physiology
Street address 111 Mason Farm Rd.
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7545
Country USA
Platform ID GPL1319
Series (1)
GSE8327 Zebrafish response to Mycobacterium marinum infection (Affymetrix series)

Data table header descriptions
RAW_VALUE a raw unnormalized measure of the abundance of a transcript
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
VALUE a normalized measure of the abundance of a transcript

Data table
AFFX-BioB-3_at 508.5 A 15.3498
AFFX-BioB-5_at 108.2 A 6.19023
AFFX-BioB-M_at 86.1 A 7.54307
AFFX-BioC-3_at 455.5 A 16.6744
AFFX-BioC-5_at 826.2 A 59.5216
AFFX-BioDn-3_at 6455.6 A 77.0335
AFFX-BioDn-5_at 252.9 A 6.29018
AFFX-CreX-3_at 14494.2 P 257.841
AFFX-CreX-5_at 9851.3 P 222.239
AFFX-DapX-3_at 111.7 A 9.33035
AFFX-DapX-5_at 76.7 A 15.3296
AFFX-DapX-M_at 125.2 A 10.6036
AFFX-Dr-AB076373-1_at 52.5 A 12.0332
AFFX-Dr-acta1-3_at 522840.2 P 5515.04
AFFX-Dr-acta1-5_at 60421.3 P 595.345
AFFX-Dr-acta1-5_x_at 111955.2 P 3940.77
AFFX-Dr-acta1-M_at 368009.7 P 4374.92
AFFX-Dr-AF292559-1_at 74.2 A 1.33858
AFFX-Dr-AF292559-2_s_at 16.8 A 7.08357
AFFX-Dr-AF292559-3_s_at 93.7 A 4.48555

Total number of rows: 15617

Table truncated, full table size 500 Kbytes.

Supplementary file Size Download File type/resource
GSM206403.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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