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| Status |
Public on May 24, 2023 |
| Title |
Dam-Dpn, larval NSCs, rep2 |
| Sample type |
SRA |
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| Source name |
3rd instar larval brains
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: 3rd instar larval brains
gal4 driver: wor-GAL4
cell type: neuroblasts (neural stem cells, NSCs)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following sample collection, genomic DNA was extracted, cut with DpnI and cut fragments isolated. DamID adaptors were ligated to the isolated DNA, fragments were digested with DpnII, and amplified via PCR before next-generation sequencing library preparation.
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 |
DNBSEQ-G400 |
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| Description |
Dpn_worG4_N2
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| Data processing |
All FASTQ files were processed with damidseq_pipeline v1.5.3, using default options and aligned to DmR6.
Peak calls were made using find_peaks v1.0.3, default options.
Assembly: DmR6
Supplementary files format and content: Score column in bedgraph files represents scaled, normalised log2 enrichment of Dam-fusion over control.
Supplementary files format and content: peaks.gff
Library strategy: DamID-seq
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| Submission date |
Feb 15, 2023 |
| Last update date |
May 24, 2023 |
| 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 |
GPL32218 |
| Series (1) |
| GSE225409 |
Dedifferentiation-derived neural stem cells exhibit perturbed temporal progression |
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| Relations |
| BioSample |
SAMN33316901 |
| SRA |
SRX19384555 |
| 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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