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Sample GSM206399 Query DataSets for GSM206399
Status Public on Jan 01, 2008
Title Wild-type_Mm-infected_rep1_10747
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: 1 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 553.2 A 19.6597
AFFX-BioB-5_at 226.5 A 14.2694
AFFX-BioB-M_at 236.5 A 8.51585
AFFX-BioC-3_at 281.6 A 20.9784
AFFX-BioC-5_at 1090.4 P 82.7942
AFFX-BioDn-3_at 4988.9 A 87.8468
AFFX-BioDn-5_at 634.2 A 12.5071
AFFX-CreX-3_at 17754.2 P 339.942
AFFX-CreX-5_at 14627.6 P 308.126
AFFX-DapX-3_at 463.1 A 7.41747
AFFX-DapX-5_at 203.8 A 7.19671
AFFX-DapX-M_at 539.8 A 9.30072
AFFX-Dr-AB076373-1_at 150.2 A 10.6695
AFFX-Dr-acta1-3_at 605462.4 P 5293.7
AFFX-Dr-acta1-5_at 16388.7 P 151.981
AFFX-Dr-acta1-5_x_at 62240.5 P 2821.84
AFFX-Dr-acta1-M_at 307921.8 P 3524.77
AFFX-Dr-AF292559-1_at 69.1 A 5.3537
AFFX-Dr-AF292559-2_s_at 308.8 A 6.66643
AFFX-Dr-AF292559-3_s_at 682.6 A 8.25865

Total number of rows: 15617

Table truncated, full table size 500 Kbytes.

Supplementary file Size Download File type/resource
GSM206399.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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