|
| Status |
Public on Jan 22, 2021 |
| Title |
Female Fru Minus R2 |
| Sample type |
SRA |
| |
|
| Source name |
Female Fru Minus
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w1118
age: 2-7 day adult
genotype: UAS-mCD8-GFP/MB247-Gal80; Fru-GAL4/TM2 or TM6B
tissue: central brain neuron
|
| Treatment protocol |
Male and female brains were dissected separately, optic lobes removed, and subjected to dissociation and flow cytometry.
|
| Growth protocol |
Flies were raised on standard cornmeal-agarose with molasses at 25C on a 12 hour light/dark cycle
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear isolation and Tn5 transposition were performed as in Buenrostro J et al., 2015 with modifications made for small numbers of cells as described in Monahan K et al. 2017.
Transposed DNA was amplified with barcoded primers in NEBNext High Fidelity 2X PCR Master Mix (NEB) and purified with Ampure XP beads (Beckman Coulter) at a ratio of 1.6uL beads per 1uL library. Purified library was eluted in 30uL of 10mM Tris-HCl pH8, 0.1mM EDTA. The quality of prepared libraries was verified with a Bioanalyzer 2100 using a high sensitivity DNA kit (Agilent). Libraries were quantified using KAPA qPCR assay (KAPA Biosystems), and multiplexed and sequenced on a NextSeq Illumina machine with 75 base pair, paired-end reads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC_FemaleFruMinus_Rep2_March2018
Profile of open chromatin
|
| Data processing |
reads were trimmed with cutadapt using the following parameters: --minimum-length 18
alignment to dm6 using bowtie2 with the following parameters: -X 1000
Aligned reads were processed with samtools to create a bam file, Picard MarkDuplicates was used to mark duplicates and samtools was used to generate a final bam file with de-duplicated reads passing a q30 quality filter
Genome_build: dm6
Supplementary_files_format_and_content: bigwig files were generated with deeptools bamCoverage
Supplementary_files_format_and_content: peak calls were generated with MACS2 by pooling replicate bam files using -nomodel -shift -0 -ext -1 -fdr 0.001.
|
| |
|
| Submission date |
Oct 19, 2020 |
| Last update date |
Jan 22, 2021 |
| Contact name |
Eleanor Josephine Clowney |
| E-mail(s) |
[email protected]
|
| Phone |
7347639036
|
| Organization name |
University of Michigan
|
| Department |
MCDB
|
| Lab |
Clowney Lab
|
| Street address |
1105 North University, 4218
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE159600 |
Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization [ATAC-seq] |
| GSE160931 |
Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization |
|
| Relations |
| BioSample |
SAMN16479013 |
| SRA |
SRX9304587 |
