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| Status |
Public on Oct 16, 2023 |
| Title |
DamKDM5_rep4 |
| Sample type |
SRA |
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| Source name |
Prothoracic gland
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| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: wandering third instar larva
cell type: Prothoracic gland
genotype: tub-Gal80[ts] ; spok-Gal4 / UAS-LT3-damkdm5
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| Treatment protocol |
No treatment
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| Growth protocol |
UAS-LT3-dam or UAS-LT3-dam-kdm5 flies were crossed with tubulin-Gal80[ts]; spok-Gal4 flies and allowed to lay eggs for 24 hrs at 18ºC. Animals were incubated at 18ºC for 5 days and subsequently moved to 29ºC for 2 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue processing was performed as previously described in Marshall et al., 2016 with the following modifications. A total of 100 wandering third instar larvae of each genotype were homogenized in 500 mM EDTA followed by DNA extraction using the Zymo Quick-DNA Miniprep Plus Kit. DpnI digestion, PCR adaptor ligation, DpnII digestion, and PCR amplification were performed as described. DNA was sonicated using a Diagenode Bioruptor Pico for 6 cycles (30-sec on/90-sec off, 4ºC) and analyzed using an Agilent Bioanalyzer. DamID adaptor removal and DNA cleanup were performed as described and samples were submitted to BGI Genomics for library construction and sequencing.
Libraries were prepared at BGI Genomics following a ChIP-seq workflow. DNA fragments were first end-repaired and dA-tailed using End Repair and A-Tailing (ERAT) enzyme. Adaptors were then ligated for sequencing and ligated DNA purified using AMPure beads. DNA was then PCR amplified with BGI primers for 8 cycles and PCR purified with AMPure beads. DNA was then homogenized, circularized, digested, and again purified. DNA was then prepared into proprietary DNA nanoballs (DNB™) for sequencing.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
DNBSEQ-G400 |
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| Description |
DamKDM5_average.bedgraph
DamKDM5_FDR0.01_processed.xlsx
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| Data processing |
Libraries were sequenced on a DNBSEQ platform with 50 bp read length and 20 M clean reads.
For Targeted DamID analyses, sequencing data were aligned to release 6 of the Drosophila melanogaster genome and processed using damidseq_pipeline as previously described (Marshall et al., 2016; Marshall & Brand, 2017).
Peaks were called using find_peaks (using the parameters fdr=0.01, min_quant=0.9) (Marshall et al., 2016) on the averaged replicates, and genes overlapping peaks identified using peaks2genes (Marshall et al., 2016).
Assembly: dm6
Supplementary files format and content: bedgraph profile of average DamKDM5 across 4 replicates normalized to 4 Dam alone replicates
Supplementary files format and content: excel file with called genes, binding score, FBgns, and gff coordinates for FDR cutoff < 0.01
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| Submission date |
Apr 05, 2023 |
| Last update date |
Oct 16, 2023 |
| Contact name |
Michael Francis Rogers |
| E-mail(s) |
michael.rogers@einsteinmed.org
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| Organization name |
Albert Einstein College of Medicine
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| Department |
Genetics
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| Lab |
Julie Secombe, Ph.D.
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| Street address |
1300 Morris Park Ave, Ullmann 809
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| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL32218 |
| Series (2) |
| GSE229076 |
Genome-winding binding profile of KDM5 in Drosophila larval prothoracic gland cells via Targeted DamID analysis |
| GSE229077 |
KDM5 binding and kdm5 null mutant differential expression profiling of Drosophila prothoracic gland cells |
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| Relations |
| BioSample |
SAMN34084992 |
| SRA |
SRX19888170 |
| 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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