NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM329400 Query DataSets for GSM329400
Status Public on Oct 16, 2008
Title Embryos injected with 50uM ERbeta2 MO biological repl. 2
Sample type RNA
 
Source name 72hpf zebrafish embryos
Organism Danio rerio
Characteristics wild type
ERbeta2 morpholinos
Treatment protocol When embryo reached 72hpf they were euthanized in MS222 and put in RNAlater solution at 4°C overnight. The samples were stored until RNA isolation at -20°C
Growth protocol Eggs were pooled from different aquaria, washed with a E3 medium and injected with ERbeta2 MO or coMO at 50uM until the 4 cell stage. After they were raised in petri dishes until 72hpf at 28°C.
Extracted molecule total RNA
Extraction protocol RNA isolation was performed with Rneasy Mini Kit, Qiagen, according to the manufacturer's instructions.
Label biotin
Label protocol biotin-labeling using a IVT Labeling Kit (Affymetrix Inc.)
 
Hybridization protocol Affymetrix Gene Expression protocol using Fragmentation Buffer (Affymetrix Inc., P/N 900371), Hybridization Mix (Affymetrix Inc., P/N 900720), Hybridization Controls and Control Oligonucleotide B2 (Affymetrix Inc., P/N 900454). Arrays were washed using an Affymetrix Fluidics Station 450 (FS450_0004 protocol)
Scan protocol Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.), according to manufacturer
Description gene expression in 72hpf zebrafish embryos
Data processing Raw data processing was performed using the Affymetrix AGCC software. After hybridization and scanning, probe cell intensities were calculated by means of the MAS5 algorithm. The data were then analyzed with Genespring. The data were normalized per chip (50th percentil) and per gene (to median). They were finally filtered by fold change (fold change data files are on the Series record).
 
Submission date Oct 10, 2008
Last update date Oct 15, 2008
Contact name Mirjam Föhlicher
E-mail(s) mirjam.froehlicher@eawag.ch
Organization name eawag
Street address überlandstrasse 133
City Dübendorf
ZIP/Postal code 8600
Country Switzerland
 
Platform ID GPL1319
Series (2)
GSE13158 The role of ERbeta2 in zebrafish neuromasts development 50uM
GSE13771 The role of ERbeta2 in zebrafish neuromasts development

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 454.783 P 0.000224668
AFFX-BioB-M_at 505.771 P 4.42873e-05
AFFX-BioB-3_at 367.513 P 0.000340305
AFFX-BioC-5_at 1038.02 P 5.16732e-05
AFFX-BioC-3_at 948.968 P 4.42873e-05
AFFX-BioDn-5_at 2584.42 P 4.42873e-05
AFFX-BioDn-3_at 5170.84 P 5.16732e-05
AFFX-CreX-5_at 11551.2 P 4.42873e-05
AFFX-CreX-3_at 18970.3 P 4.42873e-05
AFFX-DapX-5_at 84.6055 P 0.00110197
AFFX-DapX-M_at 270 P 0.000753643
AFFX-DapX-3_at 459.764 P 5.16732e-05
AFFX-LysX-5_at 22.5789 M 0.0542134
AFFX-LysX-M_at 54.3426 A 0.239063
AFFX-LysX-3_at 80.565 P 0.000224668
AFFX-PheX-5_at 17.4347 A 0.185131
AFFX-PheX-M_at 30.4314 A 0.195266
AFFX-PheX-3_at 146.919 P 0.000972149
AFFX-ThrX-5_at 40.2043 A 0.39692
AFFX-ThrX-M_at 73.9532 P 0.0012475

Total number of rows: 15617

Table truncated, full table size 575 Kbytes.




Supplementary file Size Download File type/resource
GSM329400.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM329400.CHP.gz 85.1 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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