Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1129194 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR29632900_1.fastq.gz | Fastqsanger.gz | |||
| SRR29632900_2.fastq.gz | Fastqsanger.gz | |||
| SRR29632901_1.fastq.gz | Fastqsanger.gz | |||
| SRR29632901_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 55 |
Similar Datasets
Project description:An updated representation of S. meliloti metabolism that was manually-curated and encompasses information from 240 literature sources, which includes transposon-sequencing (Tn-seq) data and Phenotype MicroArray data for wild-type and mutant strains.
2020-06-01 | MODEL2003240001 | BioModels
Project description:Subsequently, using a combination of BSA-seq, transcriptomic sequencing (RNA-seq), and proteomic sequencing approaches, we identified the candidate gene Nitab4.5_0008674g0010 that encodes dihydroneopterin aldolase as a factor associated with tobacco leaf yellowing.
2024-06-15 | PXD053162 |
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:Limited functional annotation of the Z. mobilis genome is a current barrier to both basic studies of Z. mobilis and its development as a synthetic-biology chassis. To gain insight, we collected sample-matched multiomics data including RNA-seq, transcription start site sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry across different growth conditions to improve annotation and assign functional sites in the Z. mobilis genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins.
2020-07-10 | PXD016962 | Pride
Project description:Indian sandalwood (Santalum album) is an economically important plant known for its aromatic wood. This highly valued plant has also been reported as an endangered species. Despite its economic value, the genome sequence of this plant is not yet available. In the current study,we report the draft genome sequence of sandalwood generated using Illumina HiSeq1000 sequencing platform. Genome annotation was carried out using InterProScan tool and Uniprot database,which was further facilitated using in-house RNA-Seq data. Further, we carried out in-depth proteome analysis of samples derived from four tissues viz., shoot meristem, leaf, stem and fruit using high-resolution tandem mass spectrometry. Proteogenomics analysis was performed to identify novel gene models, revise the predicted gene structures and provide experimental evidence for the predicted genes. Our analysis resulted in the identification of 72,325 peptides mapping to 10,076 genes predicted in the sandalwood genome thereby validating the expression of these gene models. Additionally, this study also provides evidence for 53 novel protein coding genes and revision of 121existing gene models.
2019-05-29 | PXD006283 | Pride
Project description:Kilian2024 - Immune cell dynamics in Cue-Induced Extended Human Colitis Model
Single-cell technologies such as scRNA-seq and flow cytometry provide critical insights into immune cell behavior in inflammatory bowel disease (IBD). However, integrating these datasets into computational models for dynamic analysis remains challenging. Here, Kilian et al., (2024) developed a deterministic ODE-based model that incorporates these technologies to study immune cell population changes in murine colitis. The model parameters were optimized to fit experimental data, ensuring an accurate representation of immune cell behavior over time. It was then validated by comparing simulations with experimental data using Pearson’s correlation and further tested on independent datasets to confirm its robustness. Additionally, the model was applied to clinical bulk RNA-seq data from human IBD patients, providing valuable insights into immune system dynamics and potential therapeutic strategies.
Figure 4c, obtained from the simulation of human colitis model is highlighted here.
This model is described in the article:
Kilian, C., Ulrich, H., Zouboulis, V.A. et al. Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease. npj Syst Biol Appl 10, 69 (2024). https://doi.org/10.1038/s41540-024-00395-9
Abstract:
Single-cell-based methods such as flow cytometry or single-cell mRNA sequencing (scRNA-seq) allow deep molecular and cellular profiling of immunological processes. Despite their high throughput, however, these measurements represent only a snapshot in time. Here, we explore how longitudinal single-cell-based datasets can be used for deterministic ordinary differential equation (ODE)-based modelling to mechanistically describe immune dynamics. We derived longitudinal changes in cell numbers of colonic cell types during inflammatory bowel disease (IBD) from flow cytometry and scRNA-seq data of murine colitis using ODE-based models. Our mathematical model generalised well across different protocols and experimental techniques, and we hypothesised that the estimated model parameters reflect biological processes. We validated this prediction of cellular turnover rates with KI-67 staining and with gene expression information from the scRNA-seq data not used for model fitting. Finally, we tested the translational relevance of the mathematical model by deconvolution of longitudinal bulk mRNA-sequencing data from a cohort of human IBD patients treated with olamkicept. We found that neutrophil depletion may contribute to IBD patients entering remission. The predictive power of IBD deterministic modelling highlights its potential to advance our understanding of immune dynamics in health and disease.
This model was curated during the Hackathon hosted by BioMed X GmbH in 2024.
2025-03-07 | MODEL2502180001 | BioModels
Project description:To investigate the genome-wide occupancies of INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060), IBH1 ChIP analysis followed by direct sequencing (ChIP-Seq) on the p35S::IBH1-GFP (IBH1OE) line and a control line p35S::GFP (GFP OE) were conducted. Antibodies against GFP in the GFP-tagged IBH1 were utilized for immunoprecipitation of the endogenous protein-DNA complex, and the obtained DNA was subjected to next generation sequencing. Observation of genome-wide occupancies of atypical bHLH, INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060)
2014-03-05 | E-GEOD-51120 | biostudies-arrayexpress
Project description:Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) provides an accurate way to depict the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However bulk sequencing entangles information from different cell types and obscures cellular heterogeneity. Here, we develop and validate Cellformer, a novel deep learning method, that deconvolutes bulk ATAC-seq into cell type-specific expression across the whole genome. Cellformer enhances the bulk ATAC-seq resolution and allows an efficient cell type specific open chromatin profiling on large size cohorts at a low cost. Applied to 191 bulk samples from 3 brain regions, Cellformer identifies cell type-specific gene regulatory mechanisms and putative mediators involved in resilient to Alzheimer’s disease (RAD), an uncommon group of cognitively healthy individuals that harbor a high pathological load of Alzheimer’s disease (AD). Cell type-resolved chromatin profiling unveils cell type specific pathways and nominates potential epigenetic mediators underlying RAD that may illuminate therapeutic opportunities to limit the cognitive impact of this highly prevalent yet incurable disease. Cellformer has been made freely and publicly available to advance analysis of high-throughput bulk ATAC-seq in future investigations.
2023-07-20 | GSE226529 | GEO
Project description:Restriction site Associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allow RAD tags to serve as genetic markers spread at a high-density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and utilizing an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second novel region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and non-model systems. Keywords: microarray genotyping
2007-01-24 | GSE5773 | GEO