|
| Status |
Public on Jan 25, 2021 |
| Title |
ovary sh_w rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Ovary
|
| Organism |
Drosophila melanogaster |
| Characteristics |
treatment: w knockdown (Control)
strain: Stock carrying UAS driven shRNA against the indicated gene crossed to hsD2G4 (Czech et al., 2013)
tissue: Ovary
cell line: NA
|
| Treatment protocol |
OSCs were treated with siRNAs.
|
| Growth protocol |
OSCs were grown at 26°C. For ovary knockdowns, flies were grown at 27°C. Ovaries were dissected from 3-5 day old flies.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
OSC pellets were lysed in Trizol. Ovaries were homogenized in Trizol. RNA was isolated using phenol/chloroform extraction.
NEBNext Poly(A) mRNA magnetic Isolation Module (NEB), followed by NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina TruSeq adapters and low-quality bases were removed using Trim galore! v0.6.4 with "--stringency 6 -q 20".
Reads matching known Drosophila viruses (https://obbard.bio.ed.ac.uk/data/Updated_Drosophila_Viruses.fas.gz) were identified using Bowtie v1.2.1.1 with "-S -n 2 -M 1 --best --strata --nomaqround --no-unal".
Remaining reads were aligned to a set of 122 transposon consensus sequences using Bowtie v1.1.2.1 and to dm6 using STAR v2.7.3a "--outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outSAMmultNmax 1 --outFilterMultimapNmax 1000 --winAnchorMultimapNmax 2000 --alignSJDBoverhangMin 1 --sjdbScore 3".
Aligned reads were counted using featureCounts with "-s 2 -O –largestOverlap -Q 50" and Ensembl (r97) gene annotations.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-separated values (tsv) files with raw counts per sample for each consensus transposon or gene.
|
| |
|
| Submission date |
Nov 04, 2020 |
| Last update date |
Jan 25, 2021 |
| Contact name |
Susanne Bornelöv |
| E-mail(s) |
susanne.bornelov@cruk.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Cancer Research UK - Cambridge Institute
|
| Lab |
Hannon
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21306 |
| Series (2) |
| GSE160859 |
Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila [RNA-Seq] |
| GSE160860 |
Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila |
|
| Relations |
| BioSample |
SAMN16666794 |
| SRA |
SRX9434507 |
