GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM215726 Query DataSets for GSM215726
Status Public on Nov 01, 2007
Title Control neonate valves -2
Sample type RNA
Source name Neonatal semilunar (aortic and pulmonary) valve leaflets
Organism Mus musculus
Characteristics Pool of semilunar valve leaflets of 3-4 wildtype neonates (mix of genders)
C57BL/6 pure genetic background
Biomaterial provider Christine Biben
Treatment protocol Neonates were sacrificed and hearts dissected. Cardiac semilunar valves were isolated under the microscope in PBS. Valve leaflets (3/valve) were collected for each valve and stored in trizol reagent on ice during the dissection then at -80.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent (Invitrogen Life Technologies, Mt Waverley, Australia) according to the manufacturer's instructions.
RNA concentration, integrity and purity were determined with an Agilent 2100 Bioanalyzer and the RNA 6000 Nano assay kit (Agilent Technologies) according to the manufacturer's instructions.
Label Phycoerythrin
Label protocol 50ng of total RNA was subjected to two cycles of in vitro amplification following the instructions of the GeneChip Two cycle cDNA synthesis kit (Affymetrix #900432). Biotinylated antisense cRNA was prepared from 10ug of amplified RNA, according to the Affymetrix Small Sample Labeling Protocol II (GeneChip Expression 3’Amplification reagents, IVT labeling kit, Affymetrix #900449).
Hybridization protocol Biotinylated cRNA was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0, following the protocol described in the Affymetrix manual.
Typically, 10ug of probe was used per chip (300 ul hybridization mix).
Scan protocol Each chip was scanned once on a GeneChip Scanner, according to manufacturer’s instructions. CEL files were acquired using GCOS (see supplementary information). CHP files were generated for deposition using Expression console.
Description Pools of 3 mutant samples (2 valves with 2-3 leaflets each, so 4-6 leaflets/mutant) and 3 wildtype littermates (6 leaflets/wildtype)
Data processing CHP files were generated from CEL files in Expression console using MAS5.0 normalisation with all probe sets scaled to TGT = 500.
Submission date Aug 07, 2007
Last update date Aug 28, 2018
Contact name Christine Biben
Phone +61 2 92958522
Fax +61 2 92958501
Organization name Victor Chang Institute
Department Developmental Biology
Lab Developmental Biology
Street address 384 Victoria Street
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
Platform ID GPL1261
Series (1)
GSE8710 Semilunar valve phenotype of Cxcr7-/- neonates
Reanalyzed by GSE119085

Data table header descriptions
VALUE signal

Data table
AFFX-BioB-5_at 28.05427 A 0.5
AFFX-BioB-M_at 2.941866 A 0.9848247
AFFX-BioB-3_at 2.653316 A 0.9915595
AFFX-BioC-5_at 2923.182 P 6.02E-05
AFFX-BioC-3_at 2444.999 P 4.43E-05
AFFX-BioDn-5_at 4817.252 P 4.43E-05
AFFX-BioDn-3_at 11303.8 P 4.43E-05
AFFX-CreX-5_at 31663.83 P 4.43E-05
AFFX-CreX-3_at 32443.69 P 4.43E-05
AFFX-DapX-5_at 21.15212 A 0.205712
AFFX-DapX-M_at 399.8706 P 0.000856509
AFFX-DapX-3_at 2487.371 P 4.43E-05
AFFX-LysX-5_at 41.77976 A 0.1021454
AFFX-LysX-M_at 104.1854 P 0.01518256
AFFX-LysX-3_at 580.7463 P 5.17E-05
AFFX-PheX-5_at 45.72746 A 0.1952458
AFFX-PheX-M_at 137.8678 P 0.02392876
AFFX-PheX-3_at 522.0713 P 4.43E-05
AFFX-ThrX-5_at 46.35505 A 0.275146
AFFX-ThrX-M_at 76.33594 P 0.004014469

Total number of rows: 45101

Table truncated, full table size 1427 Kbytes.

Supplementary file Size Download File type/resource
GSM215726.CEL.gz 3.0 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