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Sample GSM215723 Query DataSets for GSM215723
Status Public on Nov 01, 2007
Title Cxcr7-/- 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 Cxcr7-/- 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 6.405133 A 0.8433528
AFFX-BioB-M_at 1.412047 A 0.9950051
AFFX-BioB-3_at 2.387246 A 0.9984087
AFFX-BioC-5_at 5164.956 P 6.02E-05
AFFX-BioC-3_at 3920.954 P 4.43E-05
AFFX-BioDn-5_at 8053.042 P 4.43E-05
AFFX-BioDn-3_at 17098.95 P 4.43E-05
AFFX-CreX-5_at 55829.97 P 5.17E-05
AFFX-CreX-3_at 54293.03 P 4.43E-05
AFFX-DapX-5_at 380.8197 P 7.01E-05
AFFX-DapX-M_at 3322.627 P 5.17E-05
AFFX-DapX-3_at 9047.252 P 4.43E-05
AFFX-LysX-5_at 79.13278 P 0.006183304
AFFX-LysX-M_at 349.9674 P 0.00010954
AFFX-LysX-3_at 1200.095 P 4.43E-05
AFFX-PheX-5_at 229.6877 P 0.000258067
AFFX-PheX-M_at 710.0058 P 0.000258358
AFFX-PheX-3_at 1413.082 P 4.43E-05
AFFX-ThrX-5_at 127.614 P 0.007620031
AFFX-ThrX-M_at 584.5765 P 5.17E-05

Total number of rows: 45101

Table truncated, full table size 1425 Kbytes.




Supplementary file Size Download File type/resource
GSM215723.CEL.gz 3.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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