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| Status |
Public on Dec 17, 2020 |
| Title |
ATAC-seq 24h 9/26/17 |
| Sample type |
SRA |
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| Source name |
optic lobe
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: L3 lamina neurons
genotype: WT
developmental stage: 24h APF
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Upon dissociation, GFP-labeled L3 neurons were FACS sorted directly into 50 μL of lysis buffer (10 mM Tris-HCl ph7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, the nuclei were spun down at 800 g for 10 min at 4°C and the supernatant was carefully removed. The pellet was resuspended in the transposase reaction mix (25 μL of 2×TD buffer [Illumina Nextera DNA Library Prep kit], 2.5 μL of Transposase [Illumina Nextera DNA Library Prep kit] and 22.5 μL of nuclease-free water) and incubated at 37°C for 30 min. Following the transposition, the DNA sample was purified with Qiagen MinElute kit.
DNA libraries were constructed using Illumina Nextera protocols
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw sequence reads were evaluated for quality using FASTQC.
Reads were filtered and trimmed with Atropos.
High quality reads were mapped to the Ensembl build BDGP6 of the D. melanogaster genome using Bowtie2.
To call the peaks we used MACS2 v2.1.1 (43) with parameters “-g dm --nomodel --nolambda --keep-dup all”, and peaks were filtered based on default settings and false discovery rate (FDR) < 0.05.
Peaks were annotated to the nearest genes and to genomic elements such as transcription start sites (TSS), transcription termination sites (TTS), exons and introns using the R Bioconductor package ChIPseeker.
Genome_build: Ensembl build BDGP6
Supplementary_files_format_and_content: The bw files are the peak files for each sample
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| Submission date |
Dec 16, 2020 |
| Last update date |
Dec 20, 2020 |
| Contact name |
Jing Peng |
| E-mail(s) |
[email protected]
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| Organization name |
Harvard Medical School
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| Department |
Neurobiology
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| Lab |
David Ginty
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| Street address |
220 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE163307 |
Drosophila L3 ATAC-seq at 24h APF |
| GSE163311 |
Drosophila Fezf functions as a transcriptional repressor to direct layer specific synaptic connectivity in the fly visual system |
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| Relations |
| BioSample |
SAMN17089106 |
| SRA |
SRX9689642 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4976913_GEN00110843_combined.bw |
31.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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