|
| Status |
Public on Jun 01, 2013 |
| Title |
rde1_non_inf_2 |
| Sample type |
SRA |
| |
|
| Source name |
C.elegans whole animal, mixed stage
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
infection status: n/a
strain: rde-1
|
| Treatment protocol |
Virus was added to plates 24 hrs after seeding L4s on the plates and RNA was collected 4 days later.
|
| Growth protocol |
C. elegans were grown under standard conditions at 20C The food source used was E. coli strain HB101 (Caenorhabditis Genetics Center, University of Minnesota, Twin Cities, MN, USA). We used bleaching followed by starvation-induced L1 arrest to generate synchronized cultures. The wild-type strain was Bristol N2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA libraries were prepared by Vertis Biotechnologie AG (Martinsried). Briefly total RNA was extracted using the mirVana miRNA isolation kit (Ambion). Small RNAs were size selected to ~18-30 nucleotides by denaturing polyacrylamide gel fractionation. cDNA libraries that did not depend on 5'-monophosphates were constructed by tobacco acid pyrophosphatase treatment using adapters recommended for Illumina sequencing as described previously (Das et al. 2008). Each sample was labelled with a unique four base pair barcode. cDNA was purified using the NucleoSpin Extract II kit (Macherey & Nagel).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
smallRNA-seq
|
| Data processing |
Custom Perl scripts were used for processing and run with Perl v5.10.1. Fastq entries with missing bases or barcodes not matching any of the expected sequences were excluded. Reads were trimmed by removing 5' barcodes (if applicable) and any 3'As. Inserts with length outside the relevant size range (18-30 nucleotides) were excluded.
Supplementary_files_format_and_content: collapsed fasta files showing unique sequences.
|
| |
|
| Submission date |
Sep 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric A. Miska |
| E-mail(s) |
e.miska@gurdon.cam.ac.uk
|
| Phone |
44-1223-767221
|
| Organization name |
University of Cambridge
|
| Department |
Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We
|
| Lab |
Miska
|
| Street address |
Tennis Court Rd
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13657 |
| Series (2) |
| GSE41057 |
Changes in small RNAs upon Viral infection of C.elegans |
| GSE41058 |
Competition between viral-derived and endogenous small RNA pathways regulates gene expression in response to viral infection in C.elegans. |
|
| Relations |
| SRA |
SRX189092 |
| BioSample |
SAMN01180417 |
