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Sample GSM206405 Query DataSets for GSM206405
Status Public on Jan 01, 2008
Title Mock-infected_rep1_10756
Sample type RNA
 
Source name Whole 6dpf zebrafish larvae mock-infected at 1dpf
Organism Danio rerio
Characteristics Strain: AB, Age: 6 days post-fertilization (6dpf), Tissue: whole larvae, Rearing conditions: conventional, Microbial status: mock-infected, 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 mock-infected 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 147.5 A 14.0949
AFFX-BioB-5_at 278 A 13.1871
AFFX-BioB-M_at 194.8 A 8.54826
AFFX-BioC-3_at 562.8 A 20.4075
AFFX-BioC-5_at 1172.4 P 64.6755
AFFX-BioDn-3_at 5523.8 A 64.1395
AFFX-BioDn-5_at 423.7 A 5.0985
AFFX-CreX-3_at 14709.5 P 254.442
AFFX-CreX-5_at 10381.1 P 218.454
AFFX-DapX-3_at 349.6 A 7.62835
AFFX-DapX-5_at 35.4 A 12.1185
AFFX-DapX-M_at 412.7 A 8.02235
AFFX-Dr-AB076373-1_at 79.4 A 12.154
AFFX-Dr-acta1-3_at 484456.3 P 5492.07
AFFX-Dr-acta1-5_at 38610 P 330.718
AFFX-Dr-acta1-5_x_at 79791.8 P 3632.36
AFFX-Dr-acta1-M_at 336657.8 P 4000.93
AFFX-Dr-AF292559-1_at 78.1 A 6.12402
AFFX-Dr-AF292559-2_s_at 33.4 A 9.36376
AFFX-Dr-AF292559-3_s_at 84.8 A 3.53712

Total number of rows: 15617

Table truncated, full table size 500 Kbytes.




Supplementary file Size Download File type/resource
GSM206405.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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