|
Status |
Public on Jan 25, 2021 |
Title |
OSC H3K9me3 si-gfp rep2 |
Sample type |
SRA |
|
|
Source name |
Ovarian somatic cells (OSC)
|
Organism |
Drosophila melanogaster |
Characteristics |
treatment: GFP knockdown (Control) chip antibody: anti-H3K9me3 (Active Motif #39161; LOT: 14418003) cell line: Ovarian somatic cells (OSC)
|
Treatment protocol |
OSCs were treated with siRNAs and S2 cells were transfected with indicated plasmids
|
Growth protocol |
OSC and S2 cells were grown at 26°C
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Samples were crosslinked in formaldehyde and lysed, followed by sonication. NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB)
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
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". The single-end OSC reads were aligned to a set of 122 transposon consensus sequences and to the dm6 genome using Bowtie v1.2.1.1 with "-S -n 2 -M 1 --best --strata --nomaqround --no-unal". For the paired-end reads from S2 cells, Bowtie v1.2.3 was used with the additinal options "-y --maxins 500 --fr --allow-contain". PCR duplicates were removed using MarkDuplicates from Picard tools v2.21.2. BigWig files were constructed using bamCoverage from deepTools with "--binSize 1 --ignoreForNormalization chrM --normalizeUsing CPM --centerReads --exactScaling" and either "--extendReads 260" for single-end or "--extendReads" for paired-end data. Genome_build: dm6 Supplementary_files_format_and_content: BigWig files with either all mapped reads or uniquely mapped reads only.
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|
|
Submission date |
Nov 04, 2020 |
Last update date |
Jan 26, 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) |
GSE160855 |
Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila [ChIP-Seq] |
GSE160860 |
Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila |
|
Relations |
BioSample |
SAMN16666695 |
SRA |
SRX9434474 |