|
| Status |
Public on Feb 10, 2017 |
| Title |
Small RNA cloning of 10-20 nt FLAG-dmDis3l2-CM-associated RNA_32613 |
| Sample type |
SRA |
| |
|
| Source name |
RNA associated with FLAG-dmDi3l2-CM expressed in Drosophila S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: S2
sample group: Immunopurification of FLAG-dmDis3l2-CM o/n in the absence of EDTA
genotype/variation: stably expressing FLAG-dmDis3l2-CM under Actin5C promoter
molecule subtype: RNA associated with dmDis3l2-CM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Immunopurification of FLAG-dmDis3l2-CM o/n in the absence of EDTA, followed by CIP/PNK treatment and size selection of 10-20 nt RNA, RNA then subjected to small RNA cloning according to Reimao-Pinto et al, Molecular Cell, 2016
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
10-20 nt size selection
|
| Data processing |
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1). The random 4mers on 5' and 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). Summary statistics (length, nt count, nt composition from end) were computed with custom scripts for the range of 7-18nt.
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 |
GPL17275 |
| Series (1) |
| GSE84466 |
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila |
|
| Relations |
| BioSample |
SAMN05408000 |
| SRA |
SRX1951557 |
