GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM206404 Query DataSets for GSM206404
Status Public on Jan 01, 2008
Title Uninfected_rep3_10755
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: 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
Hybridization protocol Hybridization performed using standard Affymetrix protocol available at
Scan protocol Scanning performed using standard Affymetrix protocol available at
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
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 520.5 A 14.1724
AFFX-BioB-5_at 88.1 A 8.97655
AFFX-BioB-M_at 69.8 A 6.89701
AFFX-BioC-3_at 523.7 A 18.4079
AFFX-BioC-5_at 722.8 A 68.6499
AFFX-BioDn-3_at 3848.8 A 68.0827
AFFX-BioDn-5_at 450.3 A 11.3096
AFFX-CreX-3_at 17107.5 P 302.118
AFFX-CreX-5_at 9935.1 P 222.543
AFFX-DapX-3_at 57.4 A 2.65567
AFFX-DapX-5_at 275 A 9.4274
AFFX-DapX-M_at 542.7 A 9.22519
AFFX-Dr-AB076373-1_at 471.8 A 13.7871
AFFX-Dr-acta1-3_at 433451.7 P 5623.9
AFFX-Dr-acta1-5_at 14613 P 132.114
AFFX-Dr-acta1-5_x_at 43189.6 P 2637.57
AFFX-Dr-acta1-M_at 279650.9 P 3511.8
AFFX-Dr-AF292559-1_at 113.8 A 5.8837
AFFX-Dr-AF292559-2_s_at 185.5 A 5.89361
AFFX-Dr-AF292559-3_s_at 64.7 A 2.58636

Total number of rows: 15617

Table truncated, full table size 500 Kbytes.

Supplementary file Size Download File type/resource
GSM206404.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