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| Status |
Public on Feb 17, 2023 |
| Title |
Dbia_78-Pupa_bioRep-1 |
| Sample type |
SRA |
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| Source name |
Pupal wings
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| Organism |
Drosophila biarmipes |
| Characteristics |
tissue: Pupal wings
developmental stage: 78% of pupal development
Sex: Male
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| Growth protocol |
The Drosophila genome lines used in this study were maintained on standard cornmeal medium at 20ºC with a 12:12 day-night light cycle.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted and prepared as described before (GSE142176) with some modifications: dissected wings were immediately moved into cold 1x lysis buffer after rinsing. 24 0% pupal development wing discs, 14-17 wings from at least 11 individuals at 47% pupal development, and 24 wings from later stages were used for following steps, respectively. Only the pupal wings older than 60% of pupal development were cut before disruption. Samples were incubated on ice for 20-30 min before and after disruption. For tagmentation: the reaction was set up with 18 µl of Tagment DNA Buffer (Illumina #15027866) with nuclei, plus 2 µl of Tagment DNA Enzyme (Illumina #15027865).
ATAC-seq libraries were prepared as described before (GSE142176; doi: 10.1073/pnas.2004003117). The libraries were amplified by NEBNext High-Fidelity 2X PCR Master Mix (NEB Cat. M0541S) for 9-11 PCR cycles, purified by Agencourt AMPure XP beads (Beckman Coulter) with double size selection (0.5x and 2.0x), and validated by Bioanalyzer using High Sensitive DNA chip (Agilent).
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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 |
ATAC-seq libraries were processed as described (GSE142176; doi: 10.1073/pnas.2004003117): The sequenced libraries were demultiplexed, trimmed, and aligned to the reference genome UCSC dm6 using Bowtie2 with following settings: -X 2000; --fr; --very-sensitive.
The aligned reads were then filtered by Picard with the following steps: clean sam, FixMate information, MarkDuplicate. The PCR duplicates were subsequently removed by SAMtools.
BigWig files were converted from normalized bedGraph files, which were generated by MACS2 with following settings: --keep-dup all; -q 0.01; --nomodel; --shift -100; --extsize 200.
Peaking calling was performed using HOMER with following settings: -style histone -size 100 -minDist 100 -gsize 1.2e+8 -o auto.
Assembly: dm6 for D. melanogaster; GCF_000233415.1 for D. biarmipes
Supplementary files format and content: BigWig files for normalized signal track, bed files for peaks called by HOMER.
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| Submission date |
Jan 12, 2023 |
| Last update date |
Feb 17, 2023 |
| 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 |
GPL33015 |
| Series (2) |
| GSE222714 |
Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila [ATAC-seq] |
| GSE222717 |
Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila. |
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| Relations |
| BioSample |
SAMN32709024 |
| SRA |
SRX19014553 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6929272_Dbia_78-Pupa_bioRep-1.bed.gz |
741.1 Kb |
(ftp)(http) |
BED |
| GSM6929272_Dbia_78-Pupa_bioRep-1.bw |
242.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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