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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 http://pathimm.wustl.edu/~mgacore/protocols.htm
 
Hybridization protocol Hybridization performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx
Scan protocol Scanning performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx
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
E-mail(s) jfrawls@med.unc.edu
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
ID_REF
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
ID_REF RAW_VALUE ABS_CALL VALUE
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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