|
Status |
Public on Jan 25, 2021 |
Title |
ovary sh_ctp rep4 |
Sample type |
SRA |
|
|
Source name |
Ovary
|
Organism |
Drosophila melanogaster |
Characteristics |
treatment: Ctp knockdown 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 |
SAMN16666766 |
SRA |
SRX9434500 |