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| Status |
Public on May 23, 2021 |
| Title |
Photoreceptor_ATAC-seq_Rep3 |
| Sample type |
SRA |
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| Source name |
Retina
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell-type: Photoreceptor neuron
age: day 10 post eclosion
Sex: male
genotype: w;;P{w[+mC]=[UAS-GFP-Msp3 00KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]
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| Growth protocol |
Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 10 with transfer to new food every other day.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. RNA was extracted from isolated GFP-tagged photoreceptor nuclei using the method described in this manuscript
ChIP-seq libraries were made with Nugen Ovation Ultralow V2 using 2 ng of DNA as starting material. CUT&Tag librares were made following Epicypher protocol, including the IDT adapters, RNA-seq libraries were made with Nugen SoLo RNAseq system using 10 ng RNA as starting material. ATAC-seq libraries were made using IDT for Illumina primers Set A
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sanger/Illumina 1.9 used for base calling
Raw reads were trimmed to discard adapter reads and low quality reads (Q<30) using Trimmomatic settings: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:75. Additionally, Omni-ATAC and CUT&Tag reads included HEADCROP:10, and CROP:50 only for Omni-ATAC
For RNA-seq, cleaned reads were mapped to Drosophila melanogaster genome version dm6 using STAR with settings: --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
For Omni-ATAC, ChIP-seq and CUT&Tag, cleaned reads were mapped to Drosophila melanogaster genome version dm6 using Bowtie2 with settings: --sensitive
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
Bigwig files were generated using deepTools subpackage bamCoverage, and bigwig files were analyzed using multiBigwigSummary, computeMatrix, plotCorrelation, plotProfile and plotHeatmap. Dm6 refGene GTF file was used for all analysis, available at UCSC
Differential expression analysis was performed using DESeq2. Peak calling was performed with MACS2 and peak annotation was performed using HOMER.
Genome_build: UCSC Aug. 2014 - BDGP Release 6 + ISO1 MT/dm6
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| Submission date |
Mar 22, 2021 |
| Last update date |
May 23, 2021 |
| Contact name |
Vikki M Weake |
| E-mail(s) |
vweake@purdue.edu
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| Organization name |
Purdue University
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| Department |
Biochemistry
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| Lab |
Weake lab
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| Street address |
175 S University St
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| City |
West Lafayette |
| State/province |
Indiana |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platform ID |
GPL17275 |
| Series (1) |
| GSE169328 |
In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei |
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| Relations |
| BioSample |
SAMN18422875 |
| SRA |
SRX10412049 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5195797_OmniATAC_R3.bw |
56.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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