Assembling the Unassemblable
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB24348 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:De novo assembling of normalized cDNA from pooled flower of Ranunculus carpaticola for microarray design and gene expression analysis
| PRJEB8330 | ENA
Project description:Using a highly efficient and strand-specific RNA-seq method combined with a highly accurate and robust algorithm and tool we developed, TruHMM for assembling full-length transcriptomes, to profile the transcriptome of E.coli K12 under different culture conditions and growth phases, we showed that the dynamic transcriptome structures appears to be culture condition and growth phases dependent. mRNA profiles of E.coli K12 cultured under different treaments including LB (OD=0.87), Heatshock (15min, 30min, 60min), and MOPS-P(0h,2h,4h).
2013-06-21 | E-GEOD-48151 | biostudies-arrayexpress
Project description:Using a highly efficient and strand-specific RNA-seq method combined with a highly accurate and robust algorithm and tool we developed, TruHMM for assembling full-length transcriptomes, to profile the transcriptome of E.coli K12 under different culture conditions and growth phases, we showed that the dynamic transcriptome structures appears to be culture condition and growth phases dependent.
2013-06-21 | GSE48151 | GEO
Project description:scRNA-seq was used to characterise hiPSC-derived kidney organoids differentiated within fully synthetic self-assembling peptide hydrogels of variable mechanical strengths and compare these to organoids differentiated within the animal-derived matrix, Matrigel. Organoids were matured in the respective matrices until day 24 of differentiation and 6 organoids per support matrix were then pooled and dissociated using the cold-active protease from Bacillus licheniformis. Cells were processed on the 10x Genomics Chromium platform using the Single-Cell 3’ v3.1 protocol. The NextSeq500 (Illumina) was used to sequence the libraries generated and initial processing of the data was carried out using the 10X Genomic Cell Ranger v3.1.0 pipeline.
2022-10-31 | E-MTAB-11149 | biostudies-arrayexpress
Project description:Chloroplasts are the metabolically most active compartment of mature leaf cells. Their proteins are involved in essential cellular processes, such as photosynthesis, nitrogen fixation, and fatty acid synthesis. For this, chloroplast proteins have to associate with other fellow organellar proteins to form functional units, react to changing environmental conditions, or optimize efficiency of biochemical reactions. We here investigated chloroplast protein-protein interactions by a combination of complexome profiling and cross-linking mass spectrometry (CX-MS). Different detergents and MS settings were tested for developing a new workflow, which was found to produce data of improved quality when comparted to standard complexome profiling approaches. This procedure was applied to chloroplasts acclimated to increasing light intensities to investigate the role of protein-protein interactions in the adaption to these conditions.
2023-04-27 | MSV000091808 | MassIVE
Project description:The B-cell receptor (BCR) enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA-seq have enabled high throughput profiling of transcript expression in single cells, the unique task of assembling the full-length heavy and light chain sequences from single cell RNA-sequencing (scRNA-seq) in B cells has been largely unstudied. We developed a new software tool, BASIC, which allows investigators to use scRNA-seq for assembling BCR sequences at single cell level. To demonstrate the utility of our software, we subjected single B cells from a human donor to scRNA-seq, assembled the full-length heavy and the light chains, and experimentally confirmed these results by using single cell primer based nested PCRs and Sanger sequencing.
2016-06-02 | E-MTAB-4745 | biostudies-arrayexpress
Project description:Th17 cells have critical roles in mucosal defense and are major contributors to inflammatory disease. Their differentiation requires the nuclear hormone receptor RORγt working with multiple other essential transcription factors (TFs). We have used an iterative systems approach, combining genome-wide TF occupancy, expression profiling of TF mutants, and expression time series to delineate the Th17 global transcriptional regulatory network. We find that cooperatively-bound BATF and IRF4 contribute to initial chromatin accessibility, and with STAT3 initiate a transcriptional program that is then globally tuned by the lineage-specifying TF RORγt, which plays a focal deterministic role at key loci. Integration of multiple datasets allowed inference of an accurate predictive model that we computationally and experimentally validated, identifying multiple new Th17 regulators, including Fosl2, a key determinant of cellular plasticity. This interconnected network can be used to investigate new therapeutic approaches to manipulate Th17 functions in the setting of inflammatory disease. 143 RNA-seq, 83 ChIP-seq, 65 ChIP-seq controls, and 16 FAIRE-seq
2012-09-20 | E-GEOD-40918 | biostudies-arrayexpress
Project description:While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). We show that despite their derived morphology, the skate genome retains multiple features of the ancestral jawed vertebrate genome.
2023-01-12 | GSE188976 | GEO
Project description:While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). We show that despite their derived morphology, the skate genome retains multiple features of the ancestral jawed vertebrate genome.
2023-01-12 | GSE188972 | GEO