GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
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
Hybridization protocol Hybridization performed using standard Affymetrix protocol available at
Scan protocol Scanning performed using standard Affymetrix protocol available at
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
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
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
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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap