|
| Status |
Public on Jul 27, 2023 |
| Title |
control Cut n Run rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
ip target: PPI
|
| Treatment protocol |
106 S2 cells were harvested, washed and bound to pre-activated Concanavalin A-coated magnetic beads, in wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine and 1X cOmplete EDTA-free PIC)
|
| Growth protocol |
S2 cells were cultured in Schneiders Drosophila Medium until 90% confluent
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cells were then permeabilized in Antibody buffer containing 0.05% digitoninand 2 mM EDTA and incubated with rabbit α-MSL2 serum or pre-immune serum
libraries were prepared using NEBNext Ultra II DNA Library
These libraries are Cut and Run libraries
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 1000 |
| |
|
| Data processing |
RTA software von Illumina, version ist 1.18.66.3
sequenced reads were demultiplexed and trimmed using JE Demultiplexer
Demultiplexed reads were aligned to the dm6 genome using bowtie 2 version 2.2.9. with settings: -p 24 --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -X 400
filtering and sorting was done using samtools 1.9 with -q 10.
genomic tracks were made by Homer 4.9 and normalized to the negative control or the input.
replicates were summarized by subsampling them to the same read counts and summarizing them
peaks were called using findPeaks form Homer 4.9 with settings: -style factor -size 150 -F 10 -L 4
Assembly: dm6
Supplementary files format and content: .bw files
|
| |
|
| Submission date |
Apr 04, 2023 |
| Last update date |
Jul 27, 2023 |
| Contact name |
Nikolas Eggers |
| E-mail(s) |
nikolas.eggers@bmc.med.lmu.de
|
| Organization name |
LMU Munich
|
| Department |
Molecular Biology
|
| Lab |
Becker
|
| Street address |
Grosshaderner Strasse 9
|
| City |
Munich |
| ZIP/Postal code |
80469 |
| Country |
Germany |
| |
|
| Platform ID |
GPL33093 |
| Series (1) |
| GSE228935 |
MSL2 cut and run profiles in S2 cell lines |
|
| Relations |
| BioSample |
SAMN34069003 |
| SRA |
SRX19866164 |
