NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM215725 Query DataSets for GSM215725
Status Public on Nov 01, 2007
Title Control neonate valves -1
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
E-mail(s) c.biben@victorchang.edu.au
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
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE signal
ABS_CALL ABS_CALL
DETECTION P-VALUE DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 31.83225 A 0.4851099
AFFX-BioB-M_at 5.815766 A 0.9105598
AFFX-BioB-3_at 3.243733 A 0.9997033
AFFX-BioC-5_at 6840.25 P 5.17E-05
AFFX-BioC-3_at 5550.121 P 5.17E-05
AFFX-BioDn-5_at 11337.23 P 4.43E-05
AFFX-BioDn-3_at 23723.02 P 4.43E-05
AFFX-CreX-5_at 77846.46 P 5.17E-05
AFFX-CreX-3_at 74535.09 P 4.43E-05
AFFX-DapX-5_at 290.011 P 0.000509415
AFFX-DapX-M_at 3499.802 P 5.17E-05
AFFX-DapX-3_at 12669.46 P 4.43E-05
AFFX-LysX-5_at 99.75309 P 0.000752926
AFFX-LysX-M_at 520.1238 P 8.14E-05
AFFX-LysX-3_at 2103.396 P 4.43E-05
AFFX-PheX-5_at 308.3647 P 0.000445901
AFFX-PheX-M_at 913.3737 P 5.17E-05
AFFX-PheX-3_at 2103.602 P 4.43E-05
AFFX-ThrX-5_at 151.6002 P 0.006870645
AFFX-ThrX-M_at 839.1703 P 4.43E-05

Total number of rows: 45101

Table truncated, full table size 1426 Kbytes.




Supplementary file Size Download File type/resource
GSM215725.CEL.gz 2.9 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