|
| Status |
Public on Nov 18, 2019 |
| Title |
jAM_2_ES |
| Sample type |
SRA |
| |
|
| Source name |
juvenile male worms ES products pooled
|
| Organism |
Litomosoides sigmodontis |
| Characteristics |
developmental stage: juvenile
Sex: male
|
| Growth protocol |
Parasites were obtained at different time points post-infection from Meriones unguiculatus, and cultured in vitro in RPMI-1640 containing 1 mg/ml Penicilin/Streptomycin, 1 mg/ml gentamycin, and 1% D-glucose, at 37C and 5% CO2 for up to 72h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Small RNA libraries were prepared using TriLink small RNA library preparation kit (Illumina compatible), following manufacturer's recommendations.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Primers were trimmed from the raw fastq format sequence data using cutadapt software (v1.9.1; parameters -O 6 -m 16 -n 5 -q 20).
Only trimmed reads that contained the adapter, were 16nt or greater in length and were present at 2 or more copies per sample were retained.
Simple scripts were used to generate non-redundant sequence sets (collapsed) in fasta format from each sample.
Genome_build: https://parasite.wormbase.org/Litomosoides_sigmodontis_prjeb3075 version nLs.2.1
Supplementary_files_format_and_content: Processed data files contain the non-redundant trimmed sequences from each sample (sequence and counts).
|
| |
|
| Submission date |
Nov 18, 2019 |
| Last update date |
Nov 20, 2019 |
| Contact name |
Amy Buck |
| E-mail(s) |
amybucklab@gmail.com, a.buck@ed.ac.uk, sujai.kumar@ed.ac.uk
|
| Organization name |
The University of Edinburgh
|
| Department |
IIIR
|
| Lab |
Buck Lab
|
| Street address |
Ashworth Labs, Charlotte Auerbach Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3FL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL27761 |
| Series (1) |
| GSE140538 |
Comparative analysis of small RNAs released by the filarial nematode Litomosoides sigmodontis in vitro and in vivo |
|
| Relations |
| BioSample |
SAMN13319757 |
| SRA |
SRX7175176 |
