|
| Status |
Public on Jun 26, 2024 |
| Title |
ATAC_24h APF eyes, Mi-2RNAi, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
pupa eye
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: pupa eye
developmental stage: 24h APF
Sex: pooled male and female
genotype: GMR-P35/w; GMR-Gal4/+; UAS-Mi-2 RNAi/+
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissues were dissected in CUT&RUN wash buffer, then dissociated in collagenase/dispase solution for 40 minutes
Libraries were prepared using Nextera PCR primers and NEBNext High-Fidelity 2x PCR Master Mix. Libraries were amplified using 8-10 PCR cycles, then cleaned up using AMPure XP beads from Beckman Coulter. Library quality was assessed using an Agilent Tape Station.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
half males, half females
S4 300 cycle
|
| Data processing |
Raw sequencing files assessed using FastQC
Trimmomatic-0.39 used to trim adaptors and low-quality bases
Reads aligned to dm6 genome using Bowtie2.4.1 with --local --very-sensitive parameters. Max fragment size set to 1000.
Duplicates marked using picard-tools2.8.1 MarkDuplicates, and BAM files generated using samtools1.5.
Peaks called using macs2 version 2.1.2. Bigwigs and heatmaps generated using DeepTools.
Assembly: dm6
Supplementary files format and content: BigWig
|
| |
|
| Submission date |
Feb 26, 2024 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Laura Buttitta |
| Organization name |
University of Michigan
|
| Department |
Molecular, Cellular and Developmental Biology
|
| Lab |
Buttitta
|
| Street address |
1105 N University Ave
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE259302 |
Mi-2 and E93 coordinate robust cell cycle exit with terminal differentiation through enhancer decommissioning [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN40144613 |
| SRA |
SRX23751811 |
