|
| Status |
Public on Feb 11, 2019 |
| Title |
T. congolense-Infected bovine serum 1 [2873TRYP] |
| Sample type |
SRA |
| |
|
| Source name |
bovine serum
|
| Organisms |
Trypanosoma congolense; Bos taurus |
| Characteristics |
infected with: T. congolense IL3000
time point: day 19 post-infection
tissue: serum
molecule subtype: small RNA
|
| Treatment protocol |
N/A
|
| Growth protocol |
Infected cattle: cattle infected with T. congolense IL3000 and serum sampled at day 19 post-infection, at a parasitaemia of approximately 5 x 10^6 trypanosomes/m;. T. congolense sample was grown in in vitro culture (TcBSF3) and RNA extracted from ~4 x 10^7 cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were extracted using Trizol LS.
TruSeq Small RNA library preparation kit (Illumina) with 10 µL total RNA as starting material (approximately 50 ng - 1.66 µg)
Samples were enriched using 15 cycles of PCR and library products of 145-160 bp were gel purified, quantified and pooled for sequencing. The library pool was sequenced using a HiSeq 2500 with 50-base single end reads and V4 chemistry.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
2873TRYP
|
| Data processing |
SmallRNA Illumina adapter trimming and read length filtering 20-39bp using Cutadapt v1.7.1
Novoalign v3.02.12 to align the trimmed reads to T.Congolense IL3000 genome
HTSeq to quantify alignment count based on TriTrypDB-v9.0 annotation
Reads normalised to RPM (Reads per Million) alignged reads
Genome_build: TriTrypDB-9.0_TcongolenseIL3000 http://tritrypdb.org
Supplementary_files_format_and_content: HTSeq raw count and aggregated normalised RPM value
|
| |
|
| Submission date |
Nov 23, 2018 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Liam Morrison |
| E-mail(s) |
liam.morrison@roslin.ed.ac.uk
|
| Organization name |
The Roslin Institute, The University of Edinburgh
|
| Street address |
Easter Bush
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH259RG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL25839 |
| Series (1) |
| GSE122858 |
Parasite specific 7SL-derived small RNA is an effective target for diagnosis of active trypanosomiasis infection |
|
| Relations |
| BioSample |
SAMN10471703 |
| SRA |
SRX5057765 |
