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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 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 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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