|
| Status |
Public on Oct 23, 2023 |
| Title |
brain_brat_IgG_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: brain
developmental stage: L3 larvae
cell type: Type II neuroblast
genotype: brat11/bratDF
antibody: IgG
|
| Treatment protocol |
Larvae were grown at 18°C until reaching the L3 stage, then shifted to 33°C for 24 hours to induce Zld overexpression
|
| Growth protocol |
Flies were raised on standard fly food at 25 °C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed using EpiCypher reagents according to the manufacturer protocol. 50 brains were used for each CUT&RUN reaction. Overnight incubation with antibodies was performed in antibody buffer containing 0.05% digitonin. 0.5 µL anti-Zld antibody was used for CUT&RUN.
Libraries were prepared using the NEBNext Ultra II kit (NEB). During library preparation, cleanup steps were performed using a 1.1X ratio of Axygen paramagnetic beads, as recommended by EpiCypher. PCR amplification was performed with the following conditions: 98°C for 45 seconds, then 14 cycles of 98°C for 15 seconds, 60°C for 10 seconds, and a final extension of 72°C for 1 minute.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CUTandRUN_47
brain_brat_IgG_total.bw
|
| Data processing |
library strategy: CUT&RUN
Raw CUT&RUN reads were trimmed to remove adapter sequences using NGmerge version 0.3
Trimmed reads were aligned to the Drosophila melanogaster genome (version dm6) using bowtie2 with paramters -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Reads with a mapping quality < 30 and reads aligning to the mitochondrial genome or scaffolds were discarded.
Peak calling was performed using MACS2 with parameters –broad -f BAMPE –keep-dup all -g dm.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigWig files: z-scoore normalized read depth of merged replicates
|
| |
|
| Submission date |
Oct 20, 2023 |
| Last update date |
Oct 23, 2023 |
| Contact name |
Melissa M Harrison |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Wisconsin Madison
|
| Department |
Biomolecular Chemistry
|
| Lab |
1135 Biochemical Sciences Bldg
|
| Street address |
420 Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (2) |
| GSE227881 |
Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function [CUT&RUN] |
| GSE227884 |
Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function |
|
| Relations |
| BioSample |
SAMN37908595 |
| SRA |
SRX22158156 |
