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| Status |
Public on Dec 20, 2022 |
| Title |
zld-, 2.5to3, atac, 2 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: embryo
genotype: zld-
developmental stage: 2.5-3 hours after egg laying
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| Treatment protocol |
All embryos were dechorionated with 50% bleach for 2 minutes and sufficiently rinsed with water afterwards. For ATAC-seq, embryos were hand-sorted based on morphology in ice-cold PBT immediately following dechorionation using an inverted contrasting microscope as described in Chen et al., 2013.
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| Growth protocol |
All embryos were collected from population cages using apple juice plates with yeast paste, following two pre-clearings. For ATAC-seq, embryos were collected at 25°C in 30 minute-windows and aged accordingly to generate the 1-1.5, 1.5-2, 2-2.5, and 2.5-3 h AEL time points.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ATAC-seq time course experiments, the following amounts of hand-sorted embryos were used: 400 embryos (1-1.5 h AEL); 100 embryos (1.5-2 h AEL); 40 embryos (2-2.5 h AEL, 2.5-3 h AEL). Following sorting, embryos were immediately dounced in ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) with 0.1% IGEPAL CA-630 and nuclei were harvested by centrifugation. The nuclear pellet was incubated for 3 minutes on ice in ATAC resuspension buffer supplemented with 0.1% IGEPAL CA-630, 0.1% Tween-20, and 0.01% Digitonin (Promega, G9441). The reaction was stopped by adding ATAC Resuspension Buffer with 0.1% Tween-20 followed by centrifugation. Tagmentation took place at 37°C for 30 minutes at 1000 rpm in a 50 µL reaction volume containing 10 µL of 5x Tagment DNA Buffer (50 mM Tris-HCl pH 7.4, 25 mM MgCl2, 50% DMF) 16.5 µL 1x PBS, 0.5 µL 10% Tween-20, 0.5 µL 1% Digitonin, 1-2 µM assembled transposome, and water.
Accessible fragments were purified using the Monarch PCR & DNA Cleanup Kit (NEB). Libraries were constructed using Illumina Nextera Dual Indexing, and qPCR was used to prevent over-amplification as done in Corces et al., 2017.
ATAC-seq for chromatin accessibility using standard Illumina 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 |
ATAC-seq paired-end sequencing reads were aligned using bowtie2 (v.2.3.5.1) to the Drosophila melanogaster genome assembly dm6.
Aligned ATAC-seq BAM files were marked for duplicates using Picard (v.2.23.8) based on unique fragment coordinates, deduplicated, reoriented according to a Tn5 enzymatic cut correction of -4/+4 on fragment ends, filtered to contain fragment lengths no greater than 600 bp, and corrected for dovetailed reads.
Genome-wide fragment coverage was calculated and saved in BigWig format.
ATAC-seq peaks were called using MACS2 (v.2.2.7.1) with default paired-end parameters using ATAC-seq fragment coverage.
The DESeq2 package (Love et al., 2014) in R was used to compute the differential chromatin accessibility in the following comparisons at all time points: wt vs. zld-; wt vs. gd7; wt vs. cic6. The differential accessibility information is provided for all comparisons as supplemental files.
Assembly: UCSC dm6
Supplementary files format and content: BigWig, narrowPeak
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| Submission date |
Nov 27, 2022 |
| Last update date |
Dec 23, 2022 |
| Contact name |
Kaelan Joseph Brennan |
| E-mail(s) |
[email protected]
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| Phone |
8125281836
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| Organization name |
Stowers Institute for Medical Research
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| Lab |
Zeitlinger
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| Street address |
1000 East 50th Street
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| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE218848 |
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation [ATAC-seq] |
| GSE218852 |
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation |
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| Relations |
| BioSample |
SAMN31886387 |
| SRA |
SRX18393582 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6757735_zldrnai_25to3_atac_2.bw |
164.6 Mb |
(ftp)(http) |
BW |
| GSM6757735_zldrnai_25to3_atac_2_peaks.narrowPeak.gz |
1.2 Mb |
(ftp)(http) |
NARROWPEAK |
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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