|
| Status |
Public on Jan 25, 2021 |
| Title |
OSC H3K4me2 si-ctp rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Ovarian somatic cells (OSC)
|
| Organism |
Drosophila melanogaster |
| Characteristics |
treatment: Ctp knockdown
chip antibody: anti-H3K4me2 (Millipore # 07-030; LOT: 2971019)
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.
|
| |
|
| 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 |
SAMN16666707 |
| SRA |
SRX9434468 |
