Common Mitochondrial Deletions in RNA-Seq: Evaluation of Bulk, Single-Cell and Spatial Transcriptomic Datasets
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA941074 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To investigate whether large mitochondrial DNA (mtDNA) deletions can be quantified and detected using the high-throughput bioinformatics tool Splice-Break (https://github.com/brookehjelm/Splice-Break2). This dataset contains 8 human middle temporal gyrus (MTG) samples (from 4 patients) that underwent spatial transcriptomic RNA-Sequencing following 10x Genomics visium protocols as well as 2 samples (from spatial transcriptomics patient 144107/144108) that underwent bulk RNA-Sequencing (one with a ribosomal depletion library preparation and one without).
2023-10-16 | GSE226663 | GEO
Project description: Not available
| S-EPMC10874445 | biostudies-literature
Project description:10 μg 293T was spiked with different amounts ( 0.2, 0.3, 0.4, 0.5 μg) of E.coli. Performed the ablation analysis to evaluate the DNN model in DeepRTAlign. Compared DeepRTAlign with Quandenser. Compared DeepRTAlign with MaxQuant’s MBR and FragPipe’s MBR. Generalizability evaluation on simulated datasets.
2023-07-31 | PXD044222 |
Project description:Evaluation of single cell classifiers for single cell RNA-seq datasets
| PRJNA529643 | ENA
Project description:Evaluation of common profibrotic pathway across interstitial lung disease
| PRJNA967318 | ENA
Project description:Spatial transcriptomics is a rapidly advancing field, yet it lacks standardized metrics for evaluating imaging-based in situ hybridization technologies. In this study, we emphasize the importance of rigorous experimental design and standardized operating procedures (SOPs) in defining performance metrics across multiple modalities—from single-cell to spatial transcriptomics to spatial proteomics. Our Spatial Touchstone (ST) dataset, generated from six tissue types across three global sites (n=76 assays), provides a comprehensive evaluation of reproducibility, sensitivity, dynamic ranges, signal-to-noise ratio, false discovery rates, cell type annotation, and congruence with single-cell profiling. Using single-nucleus RNA sequencing (snRNA-seq) on the same formalin-fixed paraffin-embedded tissues, we created a reference for transcriptional profiles to assess cellular organization and biomarker localization. In the absence of an independent 'gold standard’ in the field, this study provides an objective assessment of technical performance through standardized protocols, Spatial Touchstone Protocols (STSOP). Our open-source software, SpatialQC, allows users to evaluate samples across all technical metrics and directly impute cell annotations from single-cell datasets. This study features the largest imaging-based spatial transcriptomics data repository available, with a total of 203 spatial profiles. It incorporates both public (n=127) and ST datasets (n=76) through the Spatial Touchstone Portal (STP), available at www.spatialtouchstone.org. This resource offers users easy access to analyze and compare their own data against an extensive collection of imaging-based datasets. We show that the ST datasets demonstrate high reproducibility (r=0.93 to 1.0) and set a new benchmark for the field. Finally, we establish metrics to evaluate and integrate imaging based multi omics data from single cell into spatial transcriptomics to spatial proteomics. The ST project provides a comprehensive, reproducible assessment across platforms and sites, establishing essential standards for imaging-based spatial multi omics (transcriptomics and proteomics) and paving the way for future research and technological advancements.
2025-07-28 | GSE277080 | GEO
Project description:Deletions and duplications in mitochondrial DNA (mtDNA) cause mitochondrial disease and accumulate in conditions such as cancer and age-related disorders, but validated high-throughput methodology that can readily detect and discriminate between these two types of events is lacking. Here we present MitoSAlt, a computational method for accurate identification, quantification and visualization of mtDNA deletions and duplications from whole genome, whole exome or transcriptome sequencing data. MitoSAlt was tested on simulated sequencing reads and human patient samples with single deletions and duplications to verify its accuracy. Application to mouse models of mtDNA maintenance disease further demonstrated the ability to detect deletions and duplications even at low levels of heteroplasmy. MitoSAlt paves the way for simple and reliable determination of mtDNA deletions and duplications across a wide range of relevant conditions and available sequencing datasets.
 
| EGAS00001004380 | EGA
Project description:We report on the analyses of four unrelated patients with de novo, overlapping, hemizygous deletions of the long arm of chromosome 10. These include two small terminal deletions (10q26.2 to 10qter), a larger terminal deletion (10q26.12 to 10qter), and an interstitial deletion (10q25.3q26.13). Single nucleotide polymorphism (SNP) studies (Illumina 550 K) established that these deletions resulted in the hemizygous loss of approximately 6.1, approximately 6.1, approximately 12.5, and approximately 7.0 Mb respectively. Additionally, these data establish that Patients 1, 2, and 3 share common, distal, hemizygous deleted regions of 6.09 Mb containing 37 RefSeq genes. Patients 3 and 4 share a 2.52 Mb deleted region corresponding to the proximal deleted region of Patient 3 and the distal deleted region of Patient 4. This common, hemizygous region contains 20 RefSeq genes including two H6 family homeobox genes (HMX2 and HMX3). Based on previous reports that Hmx2/Hmx3 knockout mice have vestibular anomalies, we propose that hemizygous deletions of HMX2 and HMX3 are responsible for the inner ear malformations observed from CT images, vestibular dysfunction, and congenital sensorineural hearing loss found in Patients 3 and 4. Four cases were identified as having hemizygous 10q deletions through g-banding. These were analyzed with SNP microarrays as well as parents (controls) for cases 1 and 4.
2009-07-01 | E-GEOD-11958 | biostudies-arrayexpress
Project description:We report on the analyses of four unrelated patients with de novo, overlapping, hemizygous deletions of the long arm of chromosome 10. These include two small terminal deletions (10q26.2 to 10qter), a larger terminal deletion (10q26.12 to 10qter), and an interstitial deletion (10q25.3q26.13). Single nucleotide polymorphism (SNP) studies (Illumina 550 K) established that these deletions resulted in the hemizygous loss of approximately 6.1, approximately 6.1, approximately 12.5, and approximately 7.0 Mb respectively. Additionally, these data establish that Patients 1, 2, and 3 share common, distal, hemizygous deleted regions of 6.09 Mb containing 37 RefSeq genes. Patients 3 and 4 share a 2.52 Mb deleted region corresponding to the proximal deleted region of Patient 3 and the distal deleted region of Patient 4. This common, hemizygous region contains 20 RefSeq genes including two H6 family homeobox genes (HMX2 and HMX3). Based on previous reports that Hmx2/Hmx3 knockout mice have vestibular anomalies, we propose that hemizygous deletions of HMX2 and HMX3 are responsible for the inner ear malformations observed from CT images, vestibular dysfunction, and congenital sensorineural hearing loss found in Patients 3 and 4.
2009-07-01 | GSE11958 | GEO