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| Status |
Public on Mar 26, 2013 |
| Title |
normal bovine foot digital skin full depth biopsy 2 |
| Sample type |
SRA |
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| Source name |
full depth skin biopsy
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| Organism |
Bos taurus |
| Characteristics |
biopsy: normal bovine foot digital skin full depth biopsy
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Trizol/chloroform extraction followed by Qiagen Rneasy clean up and polyA enrichment using Ambion poly A purist kit.
All PolyA supplied by was used into the RNase 3 fragmentation. Following sscDNA synthesis these were size selected on a polyacrylamide gel, as per the SOLID Total RNA-Seqw Kit Protocol 4452437A.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
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| Data processing |
Reads were mapped to the Bos taurus genome (Btau 4.0 accessed through http://www.ensembl.org) using Tophat (version 1.2.0 http://tophat.cbcb.umd.edu/). Across the biological replicate sets, the mean number of reads mapped for chromosomes 1-29, X and MT was for healthy skin 22,246,070 and for BDD lesions 19,801,622. Mapped regions had a median coverage of 5x and the median coverage per mapped base was approximately 3-6x.
EdgeR (Bioconductor) was used to analyse differential expression of the biological replicates (healthy skin verses digital dermatitis lesions)
The EdgeR output is available in the results file "RScholey_EdgeR common dispersion output"
Genome_build: Btau 4.0
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| Submission date |
Oct 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
rachel anne scholey |
| E-mail(s) |
rachel.scholey@manchester.ac.uk
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| Organization name |
University of Manchester
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| Street address |
Oxford road
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| City |
Manchester |
| ZIP/Postal code |
M13 9WL |
| Country |
United Kingdom |
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| Platform ID |
GPL16205 |
| Series (1) |
| GSE41732 |
Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis of lesions |
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| Relations |
| SRA |
SRX201510 |
| BioSample |
SAMN01795889 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1023356_RPKMout2.gtf.gz |
6.0 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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