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Sample GSM215724 Query DataSets for GSM215724
Status Public on Nov 01, 2007
Title Cxcr7-/- 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 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
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 2.336736 A 0.976081
AFFX-BioB-M_at 1.960112 A 0.99679
AFFX-BioB-3_at 2.408067 A 0.9992471
AFFX-BioC-5_at 5988.544 P 4.43E-05
AFFX-BioC-3_at 4842.429 P 4.43E-05
AFFX-BioDn-5_at 9708.093 P 4.43E-05
AFFX-BioDn-3_at 20556.74 P 4.43E-05
AFFX-CreX-5_at 63741.72 P 5.17E-05
AFFX-CreX-3_at 63525.22 P 4.43E-05
AFFX-DapX-5_at 374.0472 P 5.16E-05
AFFX-DapX-M_at 2333.818 P 5.17E-05
AFFX-DapX-3_at 7291.109 P 4.43E-05
AFFX-LysX-5_at 34.25557 A 0.1089586
AFFX-LysX-M_at 329.5476 P 0.000224668
AFFX-LysX-3_at 914.6513 P 5.17E-05
AFFX-PheX-5_at 208.6504 P 0.000445901
AFFX-PheX-M_at 648.6687 P 0.000195116
AFFX-PheX-3_at 1109.535 P 4.40E-05
AFFX-ThrX-5_at 126.963 P 0.001101968
AFFX-ThrX-M_at 563.0481 P 4.42E-05

Total number of rows: 45101

Table truncated, full table size 1425 Kbytes.

Supplementary file Size Download File type/resource
GSM215724.CEL.gz 3.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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