|
Status |
Public on Apr 03, 2007 |
Title |
heartgraft_Syngeneic_early_rep2. |
Sample type |
RNA |
|
|
Source name |
heart graft, Syngeneic, day 10
|
Organism |
Mus musculus |
Characteristics |
Strain: C57BL/6, Gender: male, Age: 15 weeks, Tissue: heart (transplanted graft)
|
Treatment protocol |
At Day 10 post heart transplantation, recipient mice were euthanized for examination. The graft heart tissues for RNA extraction were immediately frozen and kept at -80°C.
|
Growth protocol |
Intra-abdominal heterotopic heart transplantation was performed at 2 to 4 weeks after BMT. Heart grafts from C57BL/6 mice were transplanted into GalT BMT mice and C57BL/6 syngeneic control mice.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from graft heart tissue using RNeasy Fibrous Tissue Mini (QIAGEN) according to manufacturer's protocol.
|
Label |
biotin
|
Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
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|
|
Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized on GeneChip Mouse 430_2.0 Array. GeneChips were washed and stained using Affymetrix Hyb/Wash/Stain Kit.
|
Scan protocol |
GeneChips were scanned using GeneChip Scanner 3000.
|
Description |
Gene expression data from heart graft transplanted in syngeneic recipient
|
Data processing |
The probe set level data was analyzed with the dCHIP software (dCHIP 2006, Build date: Jul 18 2006) and only the values as determined by the model-based expression level deemed ”present” using the perfect/mis match difference correction model with single probe rejection were considered further. [dChip Expression Data File] FileName=C:\Dennis\data\tomoko\MaryK-new2expression.xls dChipVersion=dChip 2006 (DNA-Chip Analyzer), Build date: Jul 18 2006 BaselineArray=C:\Dennis\data\tomoko\J888-A-Mouse430_2-01-1 (102206).CEL ModelMethod=PM/MM difference model CheckOutlier=Single,Probe, ImageSpikeAsSingleOutlier=Yes ArrayListFile= ReplicateNotAllOutlier=No LogTransformed=No (with base 2) TruncateLowValue=Yes (to value 0) TruncateToAbsentPercent=Yes (to percent 10) PSIFileUsage=Do not use (C:\Dennis\specsU133a.psi) OutputArrayOutlierAsBlank=No OutputBothSignalAndCall=Yes OutputStandardError=Yes
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|
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Submission date |
Apr 02, 2007 |
Last update date |
Aug 28, 2018 |
Contact name |
Tomoko Doki |
E-mail(s) |
tdoki@chla.usc.edu
|
Phone |
323-669-5652
|
Fax |
323-662-1709
|
Organization name |
Childrens Hospital Los Angeles
|
Department |
Cardiothoracic Surgery Research
|
Lab |
Transplantation Biological Research Laboratory
|
Street address |
4661 Sunset Blvd.
|
City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90027 |
Country |
USA |
|
|
Platform ID |
GPL1261 |
Series (1) |
GSE7424 |
Intragraft gene expression profile associated with the induction of tolerance |
|
Relations |
Reanalyzed by |
GSE119085 |