|
| Status |
Public on Nov 27, 2020 |
| Title |
Mutant Tudor brain, small RNA, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Drosophila melanogaster |
| Characteristics |
condition: mutant Tudor
tissue: brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was done using the mirVana miRNA isolation kit
Libraries were prepared using the TruSeq Small RNA; Illumina Catalog# RS-200-0012.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
AA-M1
|
| Data processing |
Base calling was performed using casava.
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1).
Preliminary adapter trimming was performed on each of the samples to remove the Illumina TruSeq Small RNA adapter and primer sequences using Trimmomatric v0.33.
A second round of adapter trimming was performed using the mirdeep2 clip_adapters program.
QA/QC of the retrimmed data was performed with fastqc. The distribution of the trimmed reads fall into two main distributions around 22 nt and 32 nt, indicating miRNAs and piRNAs are likely sequenced.
The resulting collapsed sequences were searched first against the Drosophila melanogaster (dm) piRNA sequences obtained from piRBase v1.0. Sequences that do not have a corresponding match to piRBase were searched against mature dm miRNA sequences obtained from miRBase. Sequences that do not match either piRBase or miRBase, but are between 18-22 nt in length were matched against miRBase for partial overlaps. Anything not passing this final filter were then considered as undefined. The large majority of these undefined sequences appear to be partial rRNA sequences.
The unique piRNA sequences identified in brain and ovary were searched against the small RNA library types in order to remove piRNAs annotated by piRBase that were actually other types of small RNAs.
The files were further filtered for a minimum count of 10 sequences found across (1) all samples; (2) wild-type samples; and (3) mutant samples.
The filtered minimum count list for the mutant and wild type for the brain and ovary were then compared to determine differential expression using edgeR.
Genome_build: dm6
|
| |
|
| Submission date |
May 01, 2020 |
| Last update date |
Nov 27, 2020 |
| Contact name |
Eric Christian Rouchka |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Louisville
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
KY INBRE Bioinformatics Core
|
| Street address |
522 East Gray Street
|
| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE149748 |
piRNA analysis of tudor[1] mutant Drosophila brain and ovaries |
| GSE149750 |
piRNA and transcriptomic analysis of tudor[1] mutant Drosophila brain and ovaries |
|
| Relations |
| BioSample |
SAMN14792652 |
| SRA |
SRX8241761 |
