MARS-seq2.0 an experimental and analytical pipeline for indexed sorting combined with Single-cell RNA sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA508617 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8284590.fastq.gz | Fastqsanger.gz | |||
| SRR8284600.fastq.gz | Fastqsanger.gz | |||
| SRR8284610.fastq.gz | Fastqsanger.gz | |||
| SRR8284581.fastq.gz | Fastqsanger.gz | |||
| SRR8284591.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 30 |
Similar Datasets
Project description:Human tissues are composed of trillions of cells that populate a complex space of molecular phenotypes and functions that vary in abundance by 4-9 orders of magnitude. Relying solely on unbiased sampling to characterize cellular niches becomes non-feasible, as the marginal utility of collecting more cells is diminishing quickly. Further, in many clinical samples, the relevant cell types are scarce and efficient processing is critical. We developed an integrated pipeline for index-sorting and massively parallel single-cell RNA-seq (MARS-seq2.0) that is based on over 1 million cells sequenced with this pipeline. These include, identification of unique cell types across different tissues, diseases, and unique model systems and organisms. In addition we developed several modalities that are based on MARS-seq2.0, including genetic perturbations (CRISP-seq) and spatial reconstruction (NICHE-seq). Here we present a detailed step-by-step procedure to apply the method. We combine sub microliter reaction volumes, optimization of enzymatic mixtures and enhanced analytical pipeline (http://compgenomics.weizmann.ac.il/tanay/?page_id=672) to significantly lower cost, improve reproducibility and reduce the well-to-well contamination. Data analysis combines multiple layers of quality assessment and error detection and correction, graphically presenting key statistics of library complexity, noise distribution and sequencing saturation. Importantly, our combined FACS and single cell RNA-seq workflow enables for intuitive approaches to deplete or enrich for cell populations in a data driven manner that is essential for efficient sampling of complex tissues. The experimental protocol, from sorted plates to a ready to sequence library, takes 2 days. Sequencing and running the analytical pipeline takes another 1-2 days.
2019-05-02 | GSE123392 | GEO
Project description:Sorting nitrifying microorganism with targeted cell sorting
| PRJEB81149 | ENA
Project description:Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars. Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.
2012-05-31 | E-GEOD-37124 | biostudies-arrayexpress
Project description:Purpose: Develop an analytical pipeline for dynamic RNA-seq experiments and highlight the importance of considering surgery effect in MI-induced models Methods: Mice have undergone surgery, hearts were harvested and RNA was extracted, sequenced and analyzed by DESeq2 R package. Differentially expressed transcripts were clustered by WGCNA and then analyzed to identify enriched biological processes and transcription factors. Results: Our pipeline enabled the detection of 1027 DETs. Enriched biological processes were mainly cell signilisation and inflammatory related. IL-6 was found as a key controller of the identified TFs and DETs. Immune cells were recruited to the myocardium later post surgery and some possessed phenotypic changes.
2019-04-13 | GSE127244 | GEO
Project description:Detection of extracellular vesicles (EVs) cargoes from biofluids has drawn more attention in the field of translational and clinical medicine. EV proteomics is particularly a promising tool in discovering potential biomarkers for disease diagnosis, monitoring, and therapeutics. However, the current workflow of mass spectrometry-based EV proteome analysis is not well compatible with clinical settings due to inefficient EV isolation methods and tedious sample preparation processes. To further implement highly efficient EV proteome analysis, this study established a one-pot analytical pipeline based on a robust EV isolation approach, EV total recovery and purification (EVtrap), to detect urinary EV proteome in a rapid and sensitive manner. By incorporating solvent-driven protein capture and on-bead digestion, the one-pot EV proteomics pipeline avoided any sample transfer step and largely reduced the complexity of the peptide preparation process for bottom-up proteomic analysis. Moreover, a shorter digestion time was practicable in this novel pipeline, which enables a whole EV proteome analysis to be completed within one day. In comparison with the more time-consuming conventional workflow, the one-pot pipeline was able to obtain a higher peptide yield and identify similar numbers of unique EV proteins in 1 mL of urine. Finally, we applied the one-pot pipeline to monitor potential biomarkers in urinary EVs of bladder cancer patients. A total of 2,774 proteins and ~20,000 peptides were identified in 53 urine samples using a 15-min gradient direct data-independent acquisition (directDIA). Several known bladder cancer-associated protein markers were successfully identified and showed significantly higher abundance in patient-derived EVs. Taken altogether, our novel one-pot analytical pipeline demonstrated its potential for routine and robust EV proteomics in biomedical applications.
2023-07-24 | PXD041118 | JPOST Repository
Project description:Biospecimen Pre-analytical Variables (BPV)
| PRJNA376469 | ENA
Project description:Biospecimen Pre-analytical Variables (BPV)
| PRJNA932917 | ENA
Project description:Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars.
2012-06-01 | GSE37124 | GEO
Project description:We introduce single cell combinatorial indexed cytometry by sequencing (SCITO-seq), a single cell proteomics workflow that combines split-pool indexing and droplet-based sequencing
2021-03-31 | GSE147808 | GEO