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Status |
Public on Nov 01, 2007 |
Title |
Cxcr7-/- neonate valves – 2 |
Sample type |
RNA |
|
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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).
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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.
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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 |