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| Status |
Public on Jul 28, 2020 |
| Title |
pupal wing, D2_66hAPF_rep1 |
| Sample type |
SRA |
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| Source name |
pupal wing
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| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 66h APF
tissue: wing
strain: VK16
genotype: D2
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| Treatment protocol |
White male pupal were selected and grown at 25˚C on wet filter paper for 66h.
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| Growth protocol |
Flies were cultured at 25˚C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The protocol is modified from Omni-ATACseq. 24 pupal wings were then dissected, rinsed in cold PBS for twice, and moved into 100µl cold 1x lysis buffer. The wings were further cut into 3-4 pieces and transferred into a 2ml Dounce homogenizer. They were then disrupted by 12 strokes using pestle A, rest on ice for 5min, then 20 strokes using pestle B. After additional 10min incubation on ice, 900µl 1x wash buffer was added. 20ml syringe and 20 ½ gauge needle were employed here to separate cells from the wing cuticle. The mixture was then filtered with 40µM strainer , and centrifuged at 4°C, 1000g for 10min. Pelleted nuclei were gently resuspended with 45µl ultrapure water and counted using hemocytometer. 50000 nuclei were then centrifuged at 4°C, 1000g for 10min, resuspended with 8ml 2x Tagment DNA buffer. The tagmentation reaction followed the standard ATAC-seq protocol with minor modifications: 10ul 2X TD buffer with nuclei; 2ul Tagment DNA Enzyme; 8ul ultrapure water.
Libary was prepaire using Illunmina standard protocol.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Libraries were demultiplexed and then trimmed using trimmomatic
Libraries were then aligned to dm6 genome assembly using Bowtie2
Aligned libraries were then iltered by Picard with following steps: clean sam, FixMate information, MarkDuplicate. The PCR duplicates were subsequently removed by SAMtools
Peak calling was performed on three replicates together using MACS2 (ref) with following settings: --keep-dup all; -q 0.01; --nomodel; --shift -100; --extsize 200; -B –SPMR; --call-summits
Genome_build: dm6
Supplementary_files_format_and_content: Bigwig files were converted from corresponding bedGraph files, which were generated by MACS2 using SPMR setting.
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| Submission date |
Dec 17, 2019 |
| Last update date |
Jul 30, 2020 |
| Contact name |
Nicolas Gompel |
| Organization name |
Ludwig Maximilian University of Munich
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| Department |
Faculty of Biology
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| Street address |
Grosshaderner Str. 2
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| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platform ID |
GPL19951 |
| Series (1) |
| GSE142176 |
Evolutionary co-option of a Drosophila enhancer of the yellow gene through shared chromatin accessibility input |
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| Relations |
| BioSample |
SAMN13614607 |
| SRA |
SRX7396865 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4222134_D2_66hAPF_rep1.bw |
266.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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