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| Status |
Public on Mar 31, 2021 |
| Title |
Dam-en-n1 |
| Sample type |
SRA |
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| Source name |
dissected adult ovary
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: ovary
developmental stage: Adult
genotype/variation: en-GAL4
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Adult ovaries were dissected in PBS, and processed for DamID-seq as previously described (Marshall et al., 2016; Marshall and Brand, 2017) with the following modifications. Briefly, DNA was extracted using a Quick-DNA Miniprep plus kit (Zymo), digested with DpnI (NEB) overnight and cleaned-up with a PCR purification kit (Machery-Nagel), DamID adaptors were ligated, digested with DpnII (NEB) for 2 hours, and amplified via PCR using Advantage cDNA polymerase (Clontech).
2 µg DNA was sonicated in a Bioruptor Plus (Diagenode). DamID adaptors were removed by AlwI digestion, and 500 ng of the resulting fragments end-repaired with a mix of enzymes (T4 DNA ligase (NEB) + Klenow Fragment (NEB) + T4 polynucleotide kinase (NEB)), A-tailed with Klenow 3’ to 5’ exo- (NEB), ligated to Illumina Truseq LT adaptors using Quick Ligase enzyme (NEB) and amplified via PCR with NEBNext Hi-fidelity enzyme (NEB).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Library strategy: DamID-seq
FASTQ files were processed using damidseq_pipeline, default options.
Genome_build: DmBDGP6
Supplementary_files_format_and_content: gatc.bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution. Score represents the normalised log2(Dam-fusion/Dam) enrichment, averaged over replicates and scaled.
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| Submission date |
Jan 14, 2021 |
| Last update date |
Mar 31, 2021 |
| Contact name |
Owen Marshall |
| E-mail(s) |
owen.marshall@utas.edu.au
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| Organization name |
Menzies Institute for Medical Research
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| Street address |
17 Liverpool St
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| City |
Hobart |
| State/province |
Tas |
| ZIP/Postal code |
7000 |
| Country |
Australia |
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| Platform ID |
GPL19951 |
| Series (1) |
| GSE164866 |
Stem cell niche organisation in the Drosophila ovary requires the ECM component Perlecan |
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| Relations |
| BioSample |
SAMN17316982 |
| SRA |
SRX9852530 |
| 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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