|
| Status |
Public on Feb 10, 2017 |
| Title |
In vitro degradation of randomized RNA substrate_16558 |
| Sample type |
SRA |
| |
|
| Source name |
synthetic RNA oligo NNNN-3´
|
| Organism |
synthetic construct |
| Characteristics |
sample group: 10 sec treatment with ecoRNaseR
molecule subtype: synthetic randomized RNA NNNN3´
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10 sec treatment with ecoRNaseR, residual Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
30-40 nt size selection
|
| Data processing |
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1). The random 4mers on the 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). Sequences with exact 4nt length were counted and the reads per million for each 4mer was calculated.
library strategy: synthetic RNA seq
Genome_build: Flybase r5.57
Supplementary_files_format_and_content: TXT (RPM): tab separated text containing 4mer and it's RPM (read per million); TXT (SEQCNT) tab separated text file containing alignment position, feature, tail statistics and count; XLSX: Excel file containing summary statistics (length, nt count, nt count from 3' to 5')
|
| |
|
| Submission date |
Jul 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Rainer Burkard |
| E-mail(s) |
thomas.burkard@imba.oeaw.ac.at
|
| Organization name |
IMBA
|
| Street address |
Dr. Bohrgasse 7
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL19604 |
| Series (1) |
| GSE84466 |
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila |
|
| Relations |
| BioSample |
SAMN05407994 |
| SRA |
SRX1951551 |
