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Sample GSM206402 Query DataSets for GSM206402
Status Public on Jan 01, 2008
Title Uninfected_rep1_10753
Sample type RNA
 
Source name Whole 6dpf uninfected zebrafish larvae
Organism Danio rerio
Characteristics Strain: AB, Age: 6 days post-fertilization (6dpf), Tissue: whole larvae, Rearing conditions: conventional, Microbial status: uninfected, 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 uninfected zebrafish larvae
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 331.6 A 20.4859
AFFX-BioB-5_at 576.4 A 10.4012
AFFX-BioB-M_at 65.7 A 3.59445
AFFX-BioC-3_at 705.4 A 22.42
AFFX-BioC-5_at 839.9 A 64.8178
AFFX-BioDn-3_at 3691.1 A 77.1561
AFFX-BioDn-5_at 124.4 A 3.94554
AFFX-CreX-3_at 14082.1 P 247.331
AFFX-CreX-5_at 10090 P 221.183
AFFX-DapX-3_at 431.6 A 7.37682
AFFX-DapX-5_at 508.6 A 13.2382
AFFX-DapX-M_at 396 A 10.3818
AFFX-Dr-AB076373-1_at 117.3 A 8.256
AFFX-Dr-acta1-3_at 546759.3 P 5473.64
AFFX-Dr-acta1-5_at 46963 P 420.511
AFFX-Dr-acta1-5_x_at 96253.7 P 3657.78
AFFX-Dr-acta1-M_at 365126.4 P 4011.5
AFFX-Dr-AF292559-1_at 326.9 A 8.9501
AFFX-Dr-AF292559-2_s_at 53.9 A 7.01012
AFFX-Dr-AF292559-3_s_at 41.7 A 1.52573

Total number of rows: 15617

Table truncated, full table size 501 Kbytes.




Supplementary file Size Download File type/resource
GSM206402.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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