|
| Status |
Public on Jan 03, 2016 |
| Title |
HB101_N2 |
| Sample type |
SRA |
| |
|
| Source name |
C. elegans N2 fed HB101 E. coli, 5' dependent
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/background: N2
tissue: whole animal
e. coli food source: WT (HB101)
library construction: 5' dependent
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with TRIsure according to the manufacturer's instructions.
RNA was used to generate small RNA libraries using the NEBNext small RNA kit, according to the manufacturer's instructions.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Small RNA
|
| Data processing |
Adapter clipping (fastx toolkit).
Fastq to fasta (custom script in perl 5.12).
Trim to remove short reads <15 and longer than 33 (custom script perl v 5.12).
Collapse to unique reads (fastx toolkit).
Genome_build: N/A
Supplementary_files_format_and_content: Collapsed fasta files (header: >id_number of reads).
|
| |
|
| Submission date |
Jan 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Sarkies |
| E-mail(s) |
[email protected]
|
| Organization name |
Imperial College London
|
| Department |
MRC Clinical Sciences Centre
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15716 |
| Series (1) |
| GSE64990 |
No evidence for a C. elegans small RNA response to feeding with OxyS-expressing bacteria |
|
| Relations |
| BioSample |
SAMN03284635 |
| SRA |
SRX843767 |
