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| Status |
Public on Sep 10, 2022 |
| Title |
25, EtOH, rep4 |
| Sample type |
SRA |
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| Source name |
Fat body
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Fat body
genotype: w1118
treatment: 25C:ethanol
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| Treatment protocol |
Flies were supplemented with 10 uL of 99% ethanol once every 2 days, or supplemented with 10 uL 39.4 mm S-methoprene diluted in 99% ethanol every 2 days. Treatment was administered via volatilization.
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| Growth protocol |
All flies were reared at 25C on agar-based standard diet. Virgins were collected and divided into the appropriate conditions within 8 hours post-eclosion. Flies remained in those conditions for 25 days, at which time flies were sacrificed and dissected for fat body tissue.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fat body was harvested by dissection using 25 flies per replicate, using only those flies whose ovaries displayed the proper response to S-methoprene supplementation or temperature effect. Flies with either S-methoprene or at 25C had large, viable ovaries, whereas flies at 11C with ethanol displayed the regressed ovarian morphology characteristic of diapause.
Nuclear extraction and library preparation protocols were adapted from Cources et al., 2017 and Davie et al., 2015 using the omni-ATAC adaptation. The NEBNext™ Illumina library quantification kit from New England Biosciences was used to measure final library concentration (Ref # E7630S, lot 10013445). The Nextera™ DNA library prep kit from Illumina (Ref # 15028212, lot 20256848) was used to tagment DNA, ligate adapter sequences and amplify fragments. Adapter sequences used are available (Supplemental table X). The quality of ATAC-seq libraries was assessed via Bioanalyzer (Agilent) prior to sequencing.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
virgin female adult dissected fat body. 25 days old.
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| Data processing |
FastQC data assessment
Adapter trimming via Trimgalore! and Cutadapt
Alignment to dm6 reference genome using Bowtie2 (--no-discordant and a maximum fragment length of 1000 bp)
Mitochondrial read removal via Shell and Samtools
Conversion to .bam via Samtools
Removal of optical duplicates via Picard tools and Samtools
Peaks called using MACS2 (min.FDR cutoff 0.05 and parameters --nomodel, --shift -100, --extsize 200, --keep-dup-all and –call-summits)
Blacklisted regions removed via Bedtools intersect
Differential accessibility analyzed via DiffBind
Assembly: dm6
Supplementary files format and content: comma-separated values (.csv). Data represent the set of loci that become accessible or inaccessible in response to temperature, but not S-methoprene or juvenile hormone status.
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| Submission date |
Sep 07, 2022 |
| Last update date |
Sep 10, 2022 |
| Contact name |
Corinne Hutfilz |
| E-mail(s) |
chutfilz@gmail.com
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| Organization name |
Brown University
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| Street address |
171 Meeting St.
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| City |
Providence |
| State/province |
Rhode Island |
| ZIP/Postal code |
02912 |
| Country |
USA |
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| Platform ID |
GPL23702 |
| Series (2) |
| GSE212862 |
Multiomic Analysis of Adult Diapause in Drosophila melanogaster Identifies Hallmarks of Cellular Quiescence [ATAC-seq] |
| GSE212864 |
Multiomic Analysis of Adult Diapause in Drosophila melanogaster Identifies Hallmarks of Cellular Quiescence |
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| Relations |
| BioSample |
SAMN30718689 |
| SRA |
SRX17473046 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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