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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 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 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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