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| Status |
Public on Aug 10, 2021 |
| Title |
Adult Brain, OmniATAC ato sample 2 |
| Sample type |
SRA |
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| Source name |
Adult Brain
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Brain
developmental stage: Adult
age: 3 day
genotype: UAS-CD4tdGFP/CyO; ato-Gal4, UAS-Dcr2/TM2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
100 GFP-expressing and 15 GFP negative fly brains were dissected in PBS on ice. The brains were then centrifuged at 800 xg for 5 min, after which the supernatant was replaced by 50 μL of dispase (3 mg/mL, Sigma-Aldrich_D4818-2mg), 75 μl collagenase I (100 mg/mL, Invitrogen_17100-017), and 125 μL trypsin-EDTA (0.05%, Invitrogen_25300054). Brains were dissociated at 25°C in a Thermoshaker (Grant Bio PCMT) for 15 min at 25°C at 1,000 rpm and the solution was mixed by pipette every 5 min. After, cell suspensions were passed through a 10 μM pluriStrainer (ImTec Diagnostics_435001050) and viability was assessed by the LUNA-FL Dual Fluorescence Cell Counter. Next, 4 aliquots were made containing GFP-brains cells with/without PI (10%) and GFP-positive brains with/without PI (10%). The GFP-negative brains were used to set the gates on the machine for cell size and viability (PI), the GFP-positive brains for the GFP fluorescence, after which the GFP positive cells with PI were sorted. Between 2.6 and 11k GFP positive cells were sorted and 50k cells per negative control. After sorting, regular omni-ATAC-seq was performed as described by Corces et al. (Corces et al., 2017).
omniATAC-seq
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger ATAC (version 1.2.0) count pipeline.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils package. Read quality was then checked using FastQC. The reads were mapped to the Drosophila genome (dm6) using STAR. The outputted BAM file from STAR was then indexedand sorted using SAMtools. Using genomeCoverageBed from BedTools, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Cut&Tag samples were processed similarly to ATAC-seq samples
TaDa sequencing data were mapped back to release 6.03 of the Drosophila genome using a previously described pipelines ( Marshall and Brand, 2015). Peaks were called and mapped to genes using a custom Perl program (available at https://github.com/tonysouthall/Peak_calling_DamID)
Genome_build: dm6 (dmel_r6.16_FB2017_03)
Supplementary_files_format_and_content: gff, narrowPeak, bigWig
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| Submission date |
Aug 09, 2021 |
| Last update date |
Aug 11, 2021 |
| Contact name |
Stein Aerts |
| E-mail(s) |
stein.aerts@kuleuven.vib.be
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| Organization name |
KULeuven/VIB
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| Department |
Center for Brain & Disease Research
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| Lab |
S. Aerts Lab of Computational Biology
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| Street address |
Herestraat 49, bus 602
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| City |
LEUVEN |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
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| Platform ID |
GPL30203 |
| Series (1) |
| GSE163697 |
Decoding gene regulation in the fly brain |
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| Relations |
| BioSample |
SAMN20693753 |
| SRA |
SRX11704571 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5510273_OmniATAC_ato_sample2.RPGCnormalized.bw |
91.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data provided as supplementary file |
| Processed data provided as supplementary file |
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