|
| Status |
Public on Sep 01, 2023 |
| Title |
Steer #5 infected mid anterior lung |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
tissue total RNA
|
| Organism |
Bos taurus |
| Characteristics |
steer number: 5
tissue: mid anterior lung
infection status: FMDV infected tissue
|
| Treatment protocol |
The FMDV infection was described in Pacheco JM, Arzt J, Rodriguez LL (2010) Early events in the pathogenesis of foot-and-mouth disease in cattle after controlled aerosol exposure. Vet J 183:46–53.
|
| Growth protocol |
The animal study including the approved Institutional Animal Care and Use Committee protocol was reported in Zhu JJ, Arzt J, Puckette MC, Smoliga GR, Pacheco JM, Rodriguez LL. Mechanisms of foot-and-mouth disease virus tropism inferred from differential tissue gene expression. PLoS One. 2013 May 28;8(5):e64119.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell culture well using the RNeasy mini kit (Qiagen) following the manufacturer instructions. RNA quality was assessed using the Agilent 2100 bioanalyzer (Santa Clara, CA, USA) using an RNA nanochip. Quantification of RNA was conducted on a Nanodrop 1000 (Thermo Scientific).
|
| Label |
Cy3
|
| Label protocol |
Low input RNA two color labeling kit (Agilent Technologies) was used to lable cRNA according to the manufacturer's protocol. Pooled total RNA isolated from all infected or non-infected metacarpal skin was labeled with Cy5 as universal control. All Individual RNA samples were individually labeled with Cy3.
|
| |
|
| Channel 2 |
| Source name |
Pooled total RNA of metacarpal skin
|
| Organism |
Bos taurus |
| Characteristics |
tissue: metacarpal skin
infection status: FMDV infected tissue
|
| Treatment protocol |
The FMDV infection was described in Pacheco JM, Arzt J, Rodriguez LL (2010) Early events in the pathogenesis of foot-and-mouth disease in cattle after controlled aerosol exposure. Vet J 183:46–53.
|
| Growth protocol |
The animal study including the approved Institutional Animal Care and Use Committee protocol was reported in Zhu JJ, Arzt J, Puckette MC, Smoliga GR, Pacheco JM, Rodriguez LL. Mechanisms of foot-and-mouth disease virus tropism inferred from differential tissue gene expression. PLoS One. 2013 May 28;8(5):e64119.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell culture well using the RNeasy mini kit (Qiagen) following the manufacturer instructions. RNA quality was assessed using the Agilent 2100 bioanalyzer (Santa Clara, CA, USA) using an RNA nanochip. Quantification of RNA was conducted on a Nanodrop 1000 (Thermo Scientific).
|
| Label |
Cy5
|
| Label protocol |
Low input RNA two color labeling kit (Agilent Technologies) was used to lable cRNA according to the manufacturer's protocol. Pooled total RNA isolated from all infected or non-infected metacarpal skin was labeled with Cy5 as universal control. All Individual RNA samples were individually labeled with Cy3.
|
| |
|
| |
| Hybridization protocol |
One Cy3 labled sample was cohybrided with the Cy5 labled control in one hybridization chamber (Agilent) containing an Agilent microarray (Array design #:Agilent-019963; 4 X 44k per slide). The chambers were incubated in a incubator at 65 C in a rotating cartridge overnight. After incubation, the arrays were washed with Agilent washing buffers according to amnufacturer's protocol.
|
| Scan protocol |
After hybridization and washing, the arrays were scanned at 5 micrometer per pixel with a Cy3 to Cy5 ratio of approximately 1 using a GenPix 4000B scanner (Molecular Devices) and the images were saved as tiff files.
|
| Description |
Design Format: IS-45220-4-V1
|
| Data processing |
The expression data were extracted from the tiff files using Agilent Genpix 7.0 software and the raw data were saved as gpr files for statisitcal analysis using R with librarys(limma, MASS, statmod, splines). LOESS method was applied to normalize interarray variation with a background subtraction of 15.
The gpr files were named based on the Agilent array serial number, the array number of the slide, such as 251996310039_1, the date of the experiment, and the tissues. The normalized Cy3 results of each sample were used as gene expression levels (photon per pixel) (provided in the Matrix). Averaged Expression is the mean expression of the probe. Fold Change is the difference in expression level (fold) between compared tissues. adj.P.Val is false discover rate.
|
| |
|
| Submission date |
May 12, 2023 |
| Last update date |
Sep 01, 2023 |
| Contact name |
James Jiangtao Zhu |
| E-mail(s) |
james.zhu@usda.gov
|
| Phone |
631-323-3186
|
| Organization name |
USDA-ARS
|
| Department |
Plum Island Animal Disease Center
|
| Lab |
Foreign Animal Disease Research Unit
|
| Street address |
40550 Route 25
|
| City |
Orient Point |
| State/province |
NY |
| ZIP/Postal code |
11957 |
| Country |
USA |
| |
|
| Platform ID |
GPL33409 |
| Series (1) |
| GSE232440 |
Mechanisms of Tissue Susceptibility to FMDV Persistent Infection Based on Genes Differentially Expressed between Target and Non-target Tissues |
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