|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 17, 2023 |
Title |
Dbia_0-Pupa_bioRep-2 |
Sample type |
SRA |
|
|
Source name |
Pupal wings
|
Organism |
Drosophila biarmipes |
Characteristics |
tissue: Pupal wings developmental stage: 0% of pupal development Sex: Male
|
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.
|
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).
|
|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 1500 |
|
|
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.
|
|
|
Submission date |
Jan 12, 2023 |
Last update date |
Feb 17, 2023 |
Contact name |
Nicolas Gompel |
Organization name |
Ludwig Maximilian University of Munich
|
Department |
Faculty of Biology
|
Street address |
Grosshaderner Str. 2
|
City |
Planegg-Martinsried |
ZIP/Postal code |
82152 |
Country |
Germany |
|
|
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. |
|
Relations |
BioSample |
SAMN32709023 |
SRA |
SRX19014554 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6929273_Dbia_0-Pupa_bioRep-2.bed.gz |
971.8 Kb |
(ftp)(http) |
BED |
GSM6929273_Dbia_0-Pupa_bioRep-2.bw |
279.0 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 |
|
|
|
|
|