|
| Status |
Public on Oct 23, 2013 |
| Title |
virulent strain [V1] |
| Sample type |
SRA |
| |
|
| Source name |
infected bovine_virulent Bb strain
|
| Organism |
Babesia bovis |
| Characteristics |
pathogenicity: virulent to mammalian host
host: bovine
|
| Growth protocol |
Parasites were propagted in vivo and infected red blood cells were subsequently collected and propagated in vitro for <30 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriZOL and total RNA was purified using Qiagen quick cleanup protocol
Libraries were prepared according to Illumina's instructions using Illumina Truseqv.2 kit).
All six samples were multiplexed in a single lane with 50 cycles pair-end runs. The estimated reads per library were 25 million.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA profiling
L17_V1
|
| Data processing |
Following the sequencing process, image analysis and base calling were performed with Illumina RTA v1.13.
Reads were aligned to B. bovis T2Bo genome (www.piroplasmaDB.org) using Tophat v.2.0.4 and Bowtie v.0.12.8.
Counts were generated using htseq-count v.0.5.3p9 with the default “union” overlapping mode.
Certain genes were removed from consideration if count< 1 per 2 samples.
Differentially expressed genes pairing the samples by their biological source were identified using edgeR v.2.6.12.
Genes were considered significantly and differentially regulated if |log fold change (FC)|≥1 & false detection rate (FDR)< 5%.
Genome_build: B. bovis T2Bo genome (Piroplasmadb.org v.2.0)
Supplementary_files_format_and_content: Tab-delimited counts.txt reports counts for all samples.
|
| |
|
| Submission date |
Oct 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Audrey Oi-ting Lau |
| E-mail(s) |
laua@vetmed.wsu.edu
|
| Phone |
509-335-6072
|
| Organization name |
Washington State University
|
| Department |
Veterinary Microbiology & Pathology
|
| Street address |
PO Box 647040
|
| City |
Pullman |
| State/province |
Washington State University |
| ZIP/Postal code |
99164 |
| Country |
USA |
| |
|
| Platform ID |
GPL17815 |
| Series (1) |
| GSE51560 |
Comparative transcriptome analysis of geographically distinct virulent and attenuated Babesia bovis |
|
| Relations |
| BioSample |
SAMN02380493 |
| SRA |
SRX366888 |
