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| Status |
Public on Nov 05, 2018 |
| Title |
Sox21a-n2 |
| Sample type |
SRA |
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| Source name |
dissected adult midgut
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: gut
developmental stage: adult
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from dissected midguts via Qiagen Blood and Tissue kits as per manufacturers' instructions, digested with DpnI, DamID adaptors ligated, digested with DpnII and amplified via PCR.
DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed via AlwI digestion. Sonnicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
DamID
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| Data processing |
Library strategy: DamID
FASTQ files were processed with damidseq_pipeline, version 1.4. Biological replicates in gatc.bedgraph format were averaged, and the averaged binding tracks used for further analysis.
Genes with significant RNA pol II occupancy were called via polii.gene.call v1.0.3
Peaks were called via find_peaks v1.0.2, 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. Processed files are provided as both raw data and scaled data.
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| Submission date |
Jul 24, 2017 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE101814 |
Drosophila intestinal stem and progenitor cells are major sources and regulators of homeostatic niche signals |
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| Relations |
| BioSample |
SAMN07410619 |
| SRA |
SRX3031148 |
| 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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