|
| Status |
Public on Apr 24, 2015 |
| Title |
Uninfected (Ghanaian) human plasma |
| Sample type |
SRA |
| |
|
| Source name |
Human blood (Ghana)
|
| Organism |
Homo sapiens |
| Characteristics |
infection: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from bovine nodule fluids was purified using miRNeasy kit (Qiagen) and eluted in 50 uL of 0.1 mM EDTA. Total RNA from human serum (200 uL) or plasma (50 uL) was purified using miRCURY RNA Isolation kit - Biofluids (Exiqon) and eluted in 50 uL of 0.1 mM EDTA.
Small RNA libraries were prepared using the Illumina's TruSeq Small RNA library preparation kit (Catalogue RS-200-9002DOC). PCR products were size selected and only the 140-160 bp products were sequenced on an Illumina HiSeq 2500 instrument using v3 reagents in Edinburgh Genomics (http://genomics.ed.ac.uk)
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Primers were trimmed from the raw fastq format sequence data using cutadapt software (v1.3; parameters -O 6 -m 16 -q 20).
Only trimmed reads that contained the adapter and were present at 2 or more copies per sample were retained.
Simple scripts were used to generate non-redundant sequence sets (collapsed tag counts) in a structured format from each sample.
Genome_build: www.nematodes.org/downloads/959nematodegenomes/blast/db2/Onchocerca_ochengi_nuclear_assembly_nOo.2.0.fna.gz
Genome_build: ftp.ensembl.org/pub/release-71/fasta/bos_taurus/dna/Bos_taurus.UMD3.1.71.dna.toplevel.fa.gz
Genome_build: ftp.sanger.ac.uk/pub/pathogens/Onchocerca/volvulus/OVOC.V3.fa
Supplementary_files_format_and_content: Processed data files contain the non-redundant sequences from each sample.
|
| |
|
| Submission date |
Dec 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alasdair Ivens |
| E-mail(s) |
al.ivens@ed.ac.uk
|
| Phone |
44 131 6513605
|
| Organization name |
Centre for Immunity, Infection and Evolution
|
| Street address |
Kings Buildings
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3FL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE63933 |
Onchocerca-derived small RNAs in host nodules and serum |
|
| Relations |
| BioSample |
SAMN03254373 |
| SRA |
SRX798384 |
