Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1102268 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28757800_1.fastq.gz | Fastqsanger.gz | |||
| SRR28757800_2.fastq.gz | Fastqsanger.gz | |||
| SRR28757900_1.fastq.gz | Fastqsanger.gz | |||
| SRR28757900_2.fastq.gz | Fastqsanger.gz | |||
| SRR28758000_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 604 |
Similar Datasets
Project description:Cellular barcoding using heritable synthetic barcodes coupled to high throughput sequencing is a powerful technique for the accurate tracing of clonal lineages in a wide variety of biological contexts. Recent studies have integrated cellular barcoding with a single-cell transcriptomics readout, extending the capabilities of these lineage tracing methods to the single-cell level. However there remains a lack of scalable and standardised open-source tools to pre-process and visualise both bulk and single-cell level cellular barcoding datasets. Here, we describe bartools, an open-source R-based toolkit that streamlines the pre-processing, analysis and visualisation of synthetic cellular barcoding datasets. In addition, we developed BARtab, a portable and scalable Nextflow pipeline that automates upstream barcode extraction, quality control, filtering and enumeration from high throughput sequencing data. In addition to population-level cellular barcoding datasets, BARtab and bartools contain methods for the extraction, annotation, and visualisation of transcribed barcodes from single-cell RNA-seq and spatial transcriptomics experiments, thus extending the analytical toolbox to also support novel expressed cellular barcoding methodologies. We showcase the integrated BARtab and bartools workflow through the analysis of bulk, single-cell, and spatial transcriptomics cellular barcoding datasets.
2023-11-05 | GSE246611 | GEO
Project description:Pancreatic cancer is the 3rd most prevalent cause of cancer related deaths in United states alone, with over 55000 patients being diagnosed in 2019 alone and nearly as many succumbing to it. Late detection, lack of effective therapy and poor understanding of pancreatic cancer systemically contributes to its poor survival statistics. Obesity and high caloric intake linked co-morbidities like type 2 diabetes (T2D) have been attributed as being risk factors for a number of cancers including pancreatic cancer. Studies on gut microbiome has shown that lifestyle factors as well as diet has a huge effect on the microbial flora of the gut. Further, modulation of gut microbiome has been seen to contribute to effects of intensive insulin therapy in mice on high fat diet. In another study, abnormal gut microbiota was reported to contribute to development of diabetes in Db/Db mice. Recent studies indicate that microbiome and microbial dysbiosis plays a role in not only the onset of disease but also in its outcome. In colorectal cancer, Fusobacterium has been reported to promote therapy resistance. Certain intra-tumoral bacteria have also been shown to elicit chemo-resistance by metabolizing anti-cancerous agents. In pancreatic cancer, studies on altered gut microbiome have been relatively recent. Microbial dysbiosis has been observed to be associated with pancreatic tumor progression. Modulation of microbiome has been shown to affect response to anti-PD1 therapy in this disease as well. However, most of the studies in pancreatic cancer and microbiome have remained focused om immune modulation. In the current study, we observed that in a T2D mouse model, the microbiome changed significantly as the hyperglycemia developed in these animals. Our results further showed that, tumors implanted in the T2D mice responded poorly to Gemcitabine/Paclitaxel (Gem/Pac) standard of care compared to those in the control group. A metabolomic reconstruction of the WGS of the gut microbiota further revealed that an enrichment of bacterial population involved in drug metabolism in the T2D group.
2020-11-30 | E-MTAB-8739 | biostudies-arrayexpress
Project description:We develop CoTECH, a combinatorial barcoding method allowing for high-throughput parallel single-cell detection of chromatin occupancy and transcriptome.
2021-03-05 | GSE158435 | GEO
Project description:All the reports on insect small RNAs come from holometabolous insects. However, small RNAs of hemimetabolous insects have not yet been investigated.Study of hemimetabolous insect small RNAs could provide more insights into evolution and function of small RNAs in hemi- and holometabolous insects. The locust is an important, economically harmful hemimetabolous insect and its phase changes is an interesting phenomenon.Here, we used high-throughput sequencing to characterize and compare the small RNA transcriptomes of gregarious and solitary phases in locusts. We found abundant small RNAs and their different expression profiles in the two phases.
2009-01-16 | GSE12640 | GEO
Project description:Ssr4 was experimentally proven to be required for radial growth, aerial conidation, insect infection and virulence-related cellular events in the insect mycopathogen Beauveria bassiana. For in-depth insight into the essential role of Ssr4 in the insect mycopathogen, transcriptomic analysis was carried out via high throughput sequencing (RNA-Seq), resulting in nearly one fourth of the whole genome differentially expressed in the Dssr4 mutant versus wild-type strain.
2019-06-06 | GSE132211 | GEO
Project description:Today, swine is regarded as promising biomedical model, however, its gastrointestinal microbiome dynamics have been less investigated than that of humans or murine models . The aim of this study was to establish a high-throughput multi-omics pipeline to investigate the healthy fecal microbiome of swine and its temporal dynamics as basis for future infection studies. To this end, a homogenization protocol based on deep-frozen feces followed by integrated sample preparation for different meta-omics analyses was developed. Subsequent data integration linked microbiome composition with function, i.e. expressed proteins and secreted metabolites.
2021-02-15 | PXD020775 | Pride
Project description:a high-throughput Illumina/Solexa sequencing was conducted, 478262, 702593, 835394 and 894277 unique sRNAs was discovered from four periods of M. robertsii infection, uninfected (0h), infected for 12h, 24h and 36h. Then, 7, 7, 6 and 7 known pre-miRNAs were obtained, and 33, 58, 54 and 52 candidate novel miRNAs was detected in four periods. Further analysis showed that 24 of those candidate novel miRNAs were matched to other known insect miRNAs, while 36 of those miRNAs lacked sequence homologues of insect organisms.
2022-04-01 | GSE99322 | GEO
Project description:We report the application of single cell RNA sequencing technology for high-throughput profiling of nasal microbiome Staphylococcus epidermidis in human nasal epithelial cells.
2021-02-26 | GSE167509 | GEO
Project description:Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Processing of samples still remains largely individual and labor-intensive, hindering the assay throughput and comparability across samples. Here we present a novel method for ultra-parallelized high-throughput ChIP-seq for the systematic mapping of histone modifications and transcription factors. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), barcodes chromatin within intact nuclei extracted from different tissutal sources. Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and drastical workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation in any clinical laboratory settings, for scarce samples, and large-scale studies.
2018-03-06 | GSE111000 | GEO