|
| Status |
Public on Jun 04, 2018 |
| Title |
DGRP_25193.IR_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
eye-antennal discs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: 3rd instar-wandering
treatment: Hand Dissections
genotype: DGRP_25193
|
| Growth protocol |
Normal flyfood, 25 degrees
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Eye-antennal imaginal Disc were dissected from 3rd instar wandering larvae. The discs were immediately lysed and ATAC-seq was performed
Tn5 and nextera library prep
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC_raw_counts_31_DGRP_mergedPeaks.tsv
|
| Data processing |
Cleaning (fastq-mcf)
Mapping to the dm3 genome using bowtie2
peaks were called for each sample using macs2 callpeak with parameter -g dm (-nomodel for ATAC-seq) -keep-dup all -call-summits
Peaks were merged across the samples and the number of reads for each sample for every peak were obtained using featureCounts
The counts matrix was library size normailsed using R DESeq2
Genome_build: Drosophila melanogaster FlyBase version 5.13
Supplementary_files_format_and_content: raw_counts_matrix_30_ATAC_DGRP counts for all 30k accessible regions
|
| |
|
| Submission date |
Jul 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jelle Jacobs |
| E-mail(s) |
jelle.jacobs9255@gmail.com
|
| Organization name |
Institute of molecular Pathology
|
| Department |
VBC
|
| Lab |
Stark lab
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE101827 |
The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [ATAC-seq] |
| GSE102441 |
The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes |
|
| Relations |
| BioSample |
SAMN07411464 |
| SRA |
SRX3032263 |
