|
| Status |
Public on Jun 01, 2013 |
| Title |
MAGO_12 |
| Sample type |
SRA |
| |
|
| Source name |
C.elegans whole animal, Orsay virus infected, mixed stage
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
5' end dependence: 5' Independent (RNA treated with 5' RNA polyphosphatase (Epicentre) for 30 minutes at 37C)
genotype: sago-2(tm894); ppw-1(tm914);ppw-2(tm1120);F55A12.1(tm2686);R06C7.1(tm1414);Y49F6A.1(tm1127);ZK1248.7(tm1113);F58G1.1(tm1019);C16C10.3(tm1200);sago-1(tm1195);T22H9.3(tm1186);R04A9.2(tm1116)
tissue: whole animal
|
| Treatment protocol |
RNA was extracted from worms 4 days after infection with the Orsay virus using Trizol.
|
| 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). Uninfected animals were picked as L4s and virus laid onto the plates after 24hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA libraries were prepared from total RNA using the Illumina Truseq protocol according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Adaptors were removed with Cutadapt ver 1.0
Fastq files were converted to fasta files using a custom perl script run in Perl version 5.8.12
Fasta files were collapsed using FastX toolkit
Collapsed fasta files were trimmed so that only reads with length of 15 nucleotides or above were included, using a custom perl script run in Perl version 5.8.12
Supplementary_files_format_and_content: collapsed fasta files with adaptors removed with the header sequence number-read count_sequence
|
| |
|
| Submission date |
Oct 18, 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 |
GPL15716 |
| Series (1) |
| GSE41693 |
Analysis of small RNA response to viral infection in C.elegans |
|
| Relations |
| SRA |
SRX197354 |
| BioSample |
SAMN01768078 |
