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Sample GSM206400 Query DataSets for GSM206400
Status Public on Jan 01, 2008
Title Wild-type_Mm-infected_rep2_10748
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: 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 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 718.7 A 10.3608
AFFX-BioB-5_at 595.1 A 10.8864
AFFX-BioB-M_at 106.5 A 8.64699
AFFX-BioC-3_at 599.8 A 8.3853
AFFX-BioC-5_at 725 A 33.0255
AFFX-BioDn-3_at 4651.6 A 64.7126
AFFX-BioDn-5_at 335.5 A 9.29218
AFFX-CreX-3_at 19496.7 P 290.271
AFFX-CreX-5_at 14141.5 P 234.989
AFFX-DapX-3_at 98.9 A 6.43983
AFFX-DapX-5_at 352.7 A 7.30639
AFFX-DapX-M_at 245.3 A 9.64838
AFFX-Dr-AB076373-1_at 43.6 A 6.14458
AFFX-Dr-acta1-3_at 216120.6 P 3609.21
AFFX-Dr-acta1-5_at 2441.2 A 28.0812
AFFX-Dr-acta1-5_x_at 14312.5 P 428.931
AFFX-Dr-acta1-M_at 62279.4 P 787.382
AFFX-Dr-AF292559-1_at 62.2 A 2.74576
AFFX-Dr-AF292559-2_s_at 312.9 A 5.12803
AFFX-Dr-AF292559-3_s_at 62.4 A 3.87711

Total number of rows: 15617

Table truncated, full table size 500 Kbytes.

Supplementary file Size Download File type/resource
GSM206400.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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