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Sample GSM206401 Query DataSets for GSM206401
Status Public on Jan 01, 2008
Title Wild-type_Mm-infected_rep3_10749
Sample type RNA
Source name Whole 6dpf zebrafish larvae infected with Mycobacterium marinum wild-type strain at 1dpf
Organism Danio rerio
Characteristics Strain: AB, Age: 6 days post-fertilization (6dpf), Tissue: whole larvae, Rearing conditions: conventional, Microbial status: infected with Mycobacterium marinum wild-type strain, Days post-infection: 5, Replicate: 3 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 zebrafish larvae infected with Mycobacterium marinum wild-type strain at 1dpf
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 47.5 A 13.4231
AFFX-BioB-5_at 60.3 A 6.98071
AFFX-BioB-M_at 37 A 4.44081
AFFX-BioC-3_at 143 A 15.1451
AFFX-BioC-5_at 535.1 A 60.4759
AFFX-BioDn-3_at 2815.3 A 61.3124
AFFX-BioDn-5_at 37.3 A 4.5588
AFFX-CreX-3_at 7215.3 P 117.664
AFFX-CreX-5_at 3314.8 P 91.2601
AFFX-DapX-3_at 41.3 A 6.44008
AFFX-DapX-5_at 27.3 A 16.2527
AFFX-DapX-M_at 376.2 A 7.07839
AFFX-Dr-AB076373-1_at 93.3 A 4.82083
AFFX-Dr-acta1-3_at 346323.1 P 5709.4
AFFX-Dr-acta1-5_at 33867.6 P 334.468
AFFX-Dr-acta1-5_x_at 69547.5 P 4142.76
AFFX-Dr-acta1-M_at 262245.6 P 4090.27
AFFX-Dr-AF292559-1_at 23.3 A 5.37341
AFFX-Dr-AF292559-2_s_at 209.6 A 7.64856
AFFX-Dr-AF292559-3_s_at 203.4 A 5.15119

Total number of rows: 15617

Table truncated, full table size 499 Kbytes.

Supplementary file Size Download File type/resource
GSM206401.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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