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| Status |
Public on Oct 16, 2023 |
| Title |
kdm5[140] RG_rep3 |
| Sample type |
SRA |
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| Source name |
ring gland
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| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: wandering third instar larva
tissue: ring gland
genotype: kdm5[140]
Sex: pooled male and female
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| Treatment protocol |
No treatment
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| Growth protocol |
Flies were grown on standard media at 25ºC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA from dissected ring glands was performed according to manufacturer's instructions. Animals were matched by developmental stage of wandering third instar larva. n = 80 ring glands per replicate.
Total RNA was submitted to Novogene for library construction and sequencing. At Novogene, polyA enrichment was performed to prepare mRNA libraries. Libraries were evaluated for quality using the Agilent Bioanalyzer 2100 system. Sequencing was performed on an Illumina NovaSeq PE150 sequencing platform (2 x 150bp) cycles.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
50% males, 50% females
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| Data processing |
Novogene performed data processing including QC, reference genome mapping via Hisat2 (v2.0.5), assembly via StringTie (v1.3.3b), quantification via featureCounts (v1.5.0-p3), and differential expression analysis via DESeq2 (1.20.0)
Assembly: dm6
Supplementary files format and content: counts, FPKM, log2FoldChange differential expression, and gene characterization
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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 |
GPL25244 |
| Series (2) |
| GSE229075 |
RNA-seq profiling of Drosophila larval ring glands of kdm5 null mutants |
| GSE229077 |
KDM5 binding and kdm5 null mutant differential expression profiling of Drosophila prothoracic gland cells |
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| Relations |
| BioSample |
SAMN34084985 |
| SRA |
SRX19888177 |
| 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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