RNA sequencing data from the guts of Drosophila wildtype and CG3740/nazo double mutant 20-day-old males
Data files
Jan 18, 2024 version files 6.93 GB
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RB_SP_RNA_seq.zip
6.93 GB
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README.md
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Abstract
Lipid dyshomeostasis has been implicated in a variety of diseases ranging from obesity to neurodegenerative disorders such as Neurodegeneration with Brain Iron Accumulation (NBIA). Here, we uncover the physiological role of Nazo, the Drosophilamelanogaster homolog of the NBIA-mutated protein – c19orf12, whose function has been elusive. Ablation of Drosophila c19orf12 homologs leads to dysregulation of multiple lipid metabolism genes. nazo mutants exhibit markedly reduced gut lipid droplet and whole-body triglyceride contents. Consequently, they are sensitive to starvation and oxidative stress. Nazo is required for maintaining normal levels of Perilipin-2, an inhibitor of the lipase – Brummer. Concurrent knockdown of Brummer or overexpression of Perilipin-2 rescues the nazo phenotype, suggesting that this defect, at least in part, may arise from diminished Perilipin-2 on lipid droplets leading to aberrant Brummer-mediated lipolysis. Our findings potentially provide novel insights into the role of c19orf12 as a possible link between lipid dyshomeostasis and neurodegeneration, particularly in the context of NBIA.
README: Title: RNA Sequencing data from the guts of Drosophila wildtype and CG3740/nazo double mutant 20 day old males.
- Authors: Sreejith Perinthottathil, Rajnish Bharadwaj
- Date created: 2022-09-19
- Date modified: 2022-09-20
[Access this dataset on Dryad](Dataset DOI link)
https://doi.org/10.5061/dryad.8sf7m0csb
Dataset Title: Data for the article "Nazo, the Drosophila homolog of the NBIA-mutated protein – c19orf12, is required for
triglyceride homeostasis"Persistent Identifier: https://doi.org/10.5061/dryad.8sf7m0csb
Dataset Contributors:
- Creators: Perinthottathil Sreejith, Sara Lolo, Kristen R. Patten, Maduka Gunasinghe, Neya More, Leo J.Pallanck, Rajnish Bharadwaj
Date of Issue: 2022-09-30
Publisher: University of Rochester
Contact Information
Name: Rajnish Bharadwaj
Affiliations: Pathology and Lab Medicine, University of Rochester Medical Center
Email:
Alternative Contact: postdoctoral PI
- Name: Sreejith Perinthottathil
- Affiliations: Pathology and Lab Medicine, University of Rochester Medical Center
- ORCID ID: https://orcid.org/0000-0001-5445-3265
- Email: sreejith@urmc.rochester.edu
Additional Dataset Metadata
Acknowledgements
- Funding sources: This research was partly funded by Neurodegeneration with Brain Iron Disorders Association grant.
Dates and Locations
Dates of data collection: The samples were collected on Jan 2020 in Rochester NY
Geographic locations of data collection: Wet lab work performed at University of Rochester Medical Center. Samples were sequenced at the Genomic Resource Center, University of Rochester Medical Center.
Methodological Information
- Methods of data collection/generation: see manuscript for details Manuscript in Biorxiv: https://doi.org/10.1101/2022.09.29.510106
Nazo, the Drosophila homolog of the NBIA-mutated protein – c19orf12, is required for triglyceride homeostasis
Perinthottathil Sreejith, Sara Lolo, Kristen R. Patten, Maduka Gunasinghe, Neya More, Leo J. Pallanck, Rajnish Bharadwaj
bioRxiv 2022.09.29.510106; doi: https://doi.org/10.1101/2022.09.29.510106
The data represents the RNA sequencing results of 20-day-old male guts dissected in PBS followed by the RNA sequencing analysis as described in the manuscript.
Briefly, Total RNA was isolated from triplicates of 20 freshly dissected guts of 20-day-old WT and CG3740/nazo mutant males using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) per manufacturer’s recommendations. RNA-seq analysis was performed at UR Genomics Research Center. The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality was assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplified libraries of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina flow cell and single end reads of 75nt were generated for each sample using Illumina’s NextSeq550 sequencer.
Description of the data and file structure
File Structure:
RB_SP RNAseq> subfolder 1>deliv_Bharadwaj_021720_results> Sub folder> deSeq2> Sub Folder> Star_featureCounts> Sub folder -contains 5 files
RB_SP RNAseq> subfolder 2>deliv_Bharadwaj_021720_raw.tar > Subfolder> deliv_Bharadwaj_021720_raw> sub folder cp\ontains 6 files
Describe relationships between data files, missing data codes, other abbreviations used. Be as descriptive as possible.
Abbreviations:
* RBmut= Double Mutants
* RBWT = Wildtype
* dn= down regulated genes
* up= upregulated genes
* NormCounts = Normalized counts
* volcano = Volcano plot
File names in folder RB_SP RNAseq> subfolder 1>deliv_Bharadwaj_021720_results> Sub folder> deSeq2> Sub Folder> Star_featureCounts
1. deSeq2_counts Excel file
2. deSeq2_NormCounts Excel file
3. deSeq2_RBMut_vs_RBWT Excel file
4. deSeq2_RBMut_vs_RBWT_heatmap PDF file
5. deSeq2_rlog_NormCounts Excel file
FIle names in folder RB_SP RNAseq> subfolder 2>deliv_Bharadwaj_021720_raw.tar > Subfolder> deliv_Bharadwaj_021720_raw>
- RBmut1_R1.fastq
- RBmut2_R1.fastq
- RBmut3_R1.fastq
- RBWT1_R1.fastq
- RBWT2_R1.fastq
- RBWT3_R1.fastq
Brief description of the above files: Each folder is a FASTQ sequence trace of each replicate of either Wiltype(WT) guts or Double mutant (mut) guts.
Sharing/Access information
Description of the datasets
deSeq2_counts
Read counts for the sum of reads associated with each of the exons (feature) that “belong” to that gene detected in the RNA seq of guts in triplicate in Wildtype(WT) and Double mutant(RBmut).
deSeq2_NormCounts
Normalized counts for the number of species of genes detected in the RNA seq of guts in triplicates in Wildtype(WT) and Double mutants (RBmut) It gives the number of reads that align to a feature after correcting for sequencing depth and transcriptome composition bias. N
deSeq2_RBMut_vs_RBWT
Comparison of the expression of genes expressed in the Wildtype and Double mutant with the basemean values-the average of the normalized count values for all samples, log fold change- The change in expression of the gene, pvalues-a measure of how likely it is to get the data if no real difference existed and adjusted pvalues-The p-value adjusted (padj) column contains the p-values, adjusted for multiple testing with the Benjamini-Hochberg procedure.
deSeq2_RBMut_vs_RBWT_heatmap
Heat map of the comparison of the expression of Wildtype(RBWT) and Double mutant(RBmut)
deSeq2_rlog_NormCounts
Regularized log values of the genes expressed in the Wiltype and Double mutant guts.
Methods
The samples( guts) were dissected in ice-cold PBS and flash-frozen in liquid nitrogen followed by RNA extraction using a standard RNA extraction kit (Qiagen) before being processed.