|
| Status |
Public on Oct 19, 2015 |
| Title |
S2 cells_GFP |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
treatment: dsRNA GFP treatment control sample
genotype: wild type
age: n/a
gender: n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction performed with the miRVana miRNA Isolation Kit (#AM1560, Ambion). Small RNA sequencing libraries were constructed from an input ot 20ug total RNA.
RNA libraries were constructed as described in Newman et al. (2011)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample name: 20142
40-100 nt size selection for pre-miRNA seq; material from sample 4 and 5 pooled together (i.e., S2 cells_GFP reps 1-2)
|
| Data processing |
Basecalling RTA v1.17.21.3
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). The in vitro tailing samples were only cut on 3'. The processed reads were filtered in respect of their size selection (see sample description).
Putative contamination was filtered out by aligning to sequences of S2 viruses (derived from Genbank) with tailor (v1.0b1).
All reads were aligned to the drosophila genome (Flybase r5.55) with tailor (v1.0b1). The minimum length of exact match was 18 (miRNA) and 36 (pre-miRNA).
Counts were calculated with htseq-count (v0.6.1p1). The parameters were stranded=yes and “intersection-nonempty”. A GTF containing pre-miRNAs annotations (FlyBase r5.55) was used. The annotation was split in two halves assigned to 5' an andd 3' of each miRNA region, respectively.
Counts were normalized by the total count of miRNAs in each sample (RPM).
Instead of aligning, the in vitro tailing samples were split into substrate (first 4 nuclteotides) and tail (following sequence). Untrimmed reads and reads containing nucleotides with a quality smaller 20 (PHRED) were discarded. Counts were calculated and corrected by the input since the input sample was not expected to contain tailed substrates.
Genome_build: Flybase r5.55
Supplementary_files_format_and_content: TAB delimited text files containing the reads per million (RPM) of genome matching (GM) and prefix matching (PM) 5' fixed pre-miRNA/miRNA species; TAB delimited text files containing the in vitro substrate and their counts, input subtracted counts, fraction of untailed substrate and fraction of tailed substrate
|
| |
|
| Submission date |
Feb 23, 2015 |
| 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 |
GPL13304 |
| Series (1) |
| GSE66213 |
Uridylation of RNA-hairpins by Tailor confines the emergence of novel miRNAs in Drosophila |
|
| Relations |
| BioSample |
SAMN03366568 |
| SRA |
SRX886183 |
