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Sample GSM6929273 Query DataSets for GSM6929273
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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