Find research datasets worth reusing

opencc-by-4.0Mar 2020View details →

Link to dataset related to article "Development, application and computational analysis of high-dimensional fluorescent antibody panels for single-cell flow cytometry"

The interrogation of single cells is revolutionizing biology, especially our understanding of the immune system. Flow cytometry is still one of the most versatile and high-throughput approaches for single-cell analysis, and its capability has been recently extended to detect up to 28 colors, thus approaching the utility of cytometry by time of flight (CyTOF). However, flow cytometry suffers from autofluorescence and spreading error (SE) generated by errors in the measurement of photons mainly at red and far-red wavelengths, which limit barcoding and the detection of dim markers. Consequently, development of 28-color fluorescent antibody panels for flow cytometry is laborious and time consuming. Here, we describe the steps that are required to successfully achieve 28-color measurement capability. To do this, we provide a reference map of the fluorescence spreading errors in the 28-color space to simplify panel design and predict the success of fluorescent antibody combinations. Finally, we provide detailed instructions for the computational analysis of such complex data by existing, popular algorithms (PhenoGraph and FlowSOM). We exemplify our approach by designing a high-dimensional panel to characterize the immune system, but we anticipate that our approach can be used to design any high-dimensional flow cytometry panel of choice. The full protocol takes a few days to complete, depending on the time spent on panel design and data analysis.     link related to dataset: https://flowrepository.org/id/FR-FCM-ZYV3

opencc-by-4.0Apr 2020View details →

Single cell and immune repertoire profiling of COVID-19 patients reveal novel therapeutic candidates

COVID-19, a novel pneumonia caused by SARS-CoV-2, has rapidly become the largest threat to public health. Recent studies reported lymphocytopenia but also expansions of antigen-specific T/B cells during early-recovery stage. Here we investigated 16 early-recovery patients using scRNA-seq, HLA-genotyping and deep immune repertoire profling. Our analysis revealed 916 COVID-19-specific TCR groups enriched for a novel cytotoxic CD8+ phenotype with both resident memory (ZNF683+) and tissue exit (SIRP5) markers, and identified 114 statistically-confident virus epitopes. Further, we uncovered 374 BCR groups with somatic hypermutations and/or class switch recombinations. Molecular dynamics simulations revealed 15% of the highly expanded groups may serve as neutralizing antibodies against the virus Spike protein. Finally, we discovered that bacterial infection in COVID-19 patients may elevate monocytic myeloidderived suppressor cells via TLR4/NF!B signaling and cause disease aggravation. Together, we expect our findings and immune-receptor datasets to provide immediate therapeutic options against the pandemic of COVID-19.

opencc-zeroSep 2019View details →

Data from: A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

C. elegans is an animal with few cells, but a striking diversity of cell types. Here, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and pre-terminal cell types, mapping most single cell transcriptomes to their exact position in C. elegans' invariant lineage. Using these annotations, we find that: 1) the correlation between a cell's lineage and its transcriptome increases from mid to late gastrulation, then falls dramatically as cells in the nervous system and pharynx adopt their terminal fates; 2) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and 3) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state.

opencc-by-4.0Jul 2020View details →

Single cell transcriptomes of of primary tumors and normal endometrial derived organoids treated with DBZ

Endometrial carcinoma, the most common gynecologic cancer, develops from endometrial epithelium which is composed of secretory and ciliated cells. Pathologic classification is unreliable and there is a need for prognostic tools. We used single cell sequencing to study organoid model systems derived from normal endometrial endometrium to discover novel markers specific for endometrial ciliated or secretory cells. We performed 10X based single cell sequencing on both normal and DBZ treated organoids, and on endometrial and ovarian tumours.

CRC tumor profiled in Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

Plain text files from mgatk output of CRC tumor sample originally described in "Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling" (https://doi.org/10.1038/s41587-020-0645-6).

Selected data for Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

TF1 cell line (Figure 3) and CRC cancer (Figure 4) data from the "Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling" work.

opencc-zeroAug 2020View details →

A single-cell RNAseq atlas of Schistosoma mansoni identifies a key regulator of blood feeding

Schistosomiasis is a neglected tropical disease that infects 240 million people. With no vaccines and only one drug available, new therapeutic targets are needed. The causative agents, schistosomes, are intravascular flatworm parasites that feed on blood and lay eggs, causing pathology. The function of the parasite's various tissues in successful parasitism are poorly understood, hindering identification of novel therapeutic targets. Using single cell RNAseq we characterize 43,642 cells from the adult schistosome, identifying 68 distinct cell populations including specialized stem cells that maintain the parasite's blood-digesting gut. These stem cells express the gene hnf4, which is required for gut maintenance, blood feeding, and pathology in vivo. Together, these data provide molecular insights into the organ systems of this important pathogen and identify potential therapeutic targets.

Integrative analyses of single-cell transcriptome and immune profiling reveal clonal expansion of T cells in the blood and cerebrospinal fluid of Parkinson's disease

An increasing number of studies has indicated that the immune system plays important roles in the pathogenesis of Parkinson's disease. However, little is known about the contribution of adaptive immune responses in Parkinson's disease. Here, we performed comprehensive integrative analyses of single-cell transcriptome and immune profiling of the blood of 8 Parkinson's patients and 13 healthy controls as well as the cerebrospinal fluid of 6 Parkinson's patients, 4 Alzheimer's patients, 5 mild cognitive impairment (MCI) patients and 9 healthy controls. In total, 22 T cell subsets with distinct functions and clonalities were identified from 121,402 T cells. We observed significant clonal expansion of effector CD8+ T cells in Parkinson's patients, which formed a gradient of transcriptional states from central memory CD8+ T cells to early effector CD8+ T cells followed by terminal effector CD8+ T cells. Shared TCRs in this progression suggest TCRs may be involved in the state transition of CD8+ T cells stimulated by antigens. Notably, we also found that a group of clonally expanded cytotoxic CD4+ T cells were significantly increased in Parkinson's patients compared to controls, suggesting their cytotoxic roles in Parkinson's disease. Finally, we screened putative TCR-antigen pairs that existed in both blood and cerebrospinal fluid of patients with Parkinson's disease. These results reveal an adaptive immune response in the blood and cerebrospinal fluid of Parkinson's disease and provide novel evidence of clonal, antigen-experienced T cells patrolling in the blood and cerebrospinal fluid of Parkinson's disease.

Genome sequencing of P. tricornutum mother and daughter cultures derived from single cell and separated by 30 days of proliferation - processed datasets

Genome sequencing of P. tricornutum mother and daughter cultures derived from single cell and separated by 30 days of proliferation - processed datasets. Raw data for this experiment are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658224.   Please note that the naming of files differs from the general description on /www.ncbi.nlm.nih.gov/bioproject website and in related publication: Instead of MC1-3, the processed datasets are labelled Sc1-3 Instead of DC1.1; DC1.2 and DC1.3, the processed datasets are labelled Sc11, Sc12 and Sc14 respectively Instead of DC2.1; DC2.2 and DC2.3, the processed datasets are labelled Sc21, Sc22 and Sc24 respectively Instead of DC3.1; DC3.2 and DC3.3, the processed datasets are labelled Sc31, Sc32 and Sc33 respectively Available datasets:  .bam files with ILLUMINA reads aligned to the reference P. tricornutum v2 genome used for SNP calling  .vcf files for individual samples with SNPs called using GATK3.7.0 joint_genotyping_cohort.vcf file with SNPs called jointly for all samples using GATK4.2.1    Description of the experiment:  Whole-genome Illumina sequencing of mother and daughter cultures derived from single cell to reveal genomic changes occurring within 30 day time frame. Three independent single cells were isolated from CCAP 1055/1 culture (sample label: Pt1) to start mother cultures (MC1; MC2; MC3 . On day 30 after mother culture isolation (T1 time point), three daughter cells were isolated from each mother culture forming cultures DC11-DC33. Part of mother cultures and CCAP 1055/1 culture were harvested at T1 (Samples: Pt1T1; MC1T1; MC2T1; MC3T1) . After another 30 days (T2 time point), all cultures were harvested (Samples: Pt1T2; mother culture MC1T2 and respective daughter cultures DC11, DC12 and DC13 ; mother culture MC2T2 and respective daughter cultures DC21, DC22 and DC23; mother culture MC3T1 and respective daughter cultures DC31, DC32, DC33).

opencc-zeroOct 2020View details →

The molecular diversity of phagotrophic Euglenids examined using single-cell methods

Euglenids are a diverse group of euglenozoan flagellates that includes phototrophs, osmotrophs, andphagotrophs. Despite making up most of the phylogenetic diversity of euglenids, phagotrophs remain understudied, and recent work has focused on 'deep-branching' groups. Spirocuta is the large clade encompassing all flexible euglenids including the phototroph and primary osmotroph clades, plus various phagotrophs. Understanding the phylogenetic diversity of phagotrophic spirocutes is crucial for tracing euglenid evolution, including how phototrophs arose.We used single-cell approaches to greatly increase sampling of SSU rDNA for phagotrophic euglenids, particularly spirocutes, including the first sequences from Urceolus, Jenningsia, Chasmostoma, and Sphenomonas, and expanded coverage for Dinema and Heteronema sensu lato, amongst others. Urceolus monophyly is unconfirmed. Organisms referred to Jenningsia form two distinct clades. Heteronema vittatum and similar cells branch separately from Heteronema (c.f.) globuliferum and Teloprocta/Heteronema scaphurum, while Dinema appears as 2–3 clades. Sphenomonas is monophyletic and the deepest branch within Petalomonadida. The census of genera markedly underestimates the phylogenetic diversity of phagotrophs, but taxonomic restraint is necessary when sequences are not available from type species or reasonable surrogates. SSU rDNA phylogenies do not resolve most deep relationships within Spirocuta, but identify units of diversity to sample in future multigene analyses.

opencc-by-4.0Nov 2020View details →

Data Repository: Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes

Data repository for the scMappR manuscript: Abstract from biorXiv (https://www.biorxiv.org/content/10.1101/2020.08.24.265298v1.full). RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by integrating cell-type expression data generated by scRNA-seq and existing deconvolution methods. After benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. We found that scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small proportion of immune cells. While scMappR can work with any user supplied scRNA-seq data, we curated scRNA-seq expression matrices for &sim;100 human and mouse tissues to facilitate its use with bulk RNA-seq data alone. Overall, scMappR is a user-friendly R package that complements traditional differential expression analysis available at CRAN.

opencc-zeroDec 2019View details →

Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs

Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA gene only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid Olkasia as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by Ploeotia spp.), Lentomonas, and Keelungia form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes Rapaza, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (Anisonema and Dinema spp.), 'Heteronema II' (represented by H. vittatum), and a clade of Neometanema plus Aphagea. Among 'peranemid' phagotrophs, Chasmostoma branches with included Urceolus, and Peranema with the undescribed 'Jenningsia II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that Entosiphon is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.

opencc-by-4.0Jan 2021View details →

Differential analysis of binarized single-cell RNA sequencing data captures biological variation

Processed datasets used for binary differential analysis experiments.

opencc-zeroDec 2018View details →

Data from: Neural effects of transcranial magnetic stimulation at the single-cell level

Transcranial magnetic stimulation (TMS) can non-invasively modulate neural activity in humans. Despite three decades of research, the spatial extent of the cortical area activated by TMS is still controversial. Moreover, how TMS interacts with task-related activity during motor behavior is unknown. Here, we applied single-pulse TMS over macaque parietal cortex while recording single-unit activity at various distances from the center of stimulation during grasping. The spatial extent of TMS-induced activation is remarkably restricted, affecting the spiking activity of single neurons in an area of cortex measuring less than 2 mm in diameter. In task-related neurons, TMS evokes a transient excitation followed by reduced activity, paralleled by a significantly longer grasping time. Furthermore, TMS-induced activity and task-related activity do not summate in single neurons. These results furnish crucial experimental evidence for the neural effects of TMS at the single-cell level and uncover the neural underpinnings of behavioral effects of TMS.

opencc-zeroDec 2013View details →

Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus

Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct "genomic backbones," each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.

opencc-zeroDec 2015View details →

Data from: A single 17D Yellow Fever vaccination provides lifelong immunity; characterization of Yellow-Fever-specific neutralizing antibody and T-cell responses after vaccination

Introduction: Prompted by recent amendments of Yellow Fever (YF) vaccination guidelines from boost to single vaccination strategy and the paucity of clinical data to support this adjustment, we used the profile of the YF-specific CD8+ T-cell subset profiles after primary vaccination and neutralizing antibodies as a proxy for potentially longer lasting immunity. Methods and Findings: PBMCs and serum were collected in six individuals on days 0, 3, 5, 12, 28 and 180, and in 99 individuals >10 years after YF-vaccination. Phenotypic characteristics of YF- tetramer+ CD8+ T-cells were determined using class I tetramers. Antibody responses were measured using a standardized plaque reduction neutralization test (PRNT). Also, characteristics of YF-tetramer positive CD8+ T-cells were compared between individuals who had received a primary- and a booster vaccination. YF-tetramer+ CD8+ T-cells were detectable on day 12 (median tetramer+ cells as percentage of CD8+ T-cells 0.2%, range 0.07–3.1%). On day 180, these cells were still present (median 0.06%, range 0.02–0.78%). The phenotype of YF-tetramer positive CD8+ T-cells shifted from acute phase effector cells on day 12, to late differentiated or effector memory phenotype (CD45RA-/+CD27-) on day 28. Two subsets of YF-tetramer positive T-cells (CD45RA+CD27- and CD45RA+CD27+) persisted until day 180. Within all phenotypic subsets, the T-bet: Eomes ratio tended to be high on day 28 after vaccination and shifted towards predominant Eomes expression on day 180 (median 6.0 (day 28) vs. 2.2 (day 180) p = 0.0625), suggestive of imprinting compatible with long-lived memory properties. YF-tetramer positive CD8+ T-cells were detectable up to 18 years post vaccination, YF-specific antibodies were detectable up to 40 years after single vaccination. Booster vaccination did not increase titers of YF-specific antibodies (mean 12.5 vs. 13.1, p = 0.583), nor induce frequencies or alter phenotypes of YF-tetramer+ CD8+ T-cells. Conclusion: The presence of a functionally competent YF-specific memory T-cell pool 18 years and sufficient titers of neutralizing antibodies 35–40 years after first vaccination suggest that single vaccination may be sufficient to provide long-term immunity.

opencc-zeroDec 2014View details →

Data from: Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1)IB4+SNS-Cre/TdTomato+, 2)IB4-SNS-Cre/TdTomato+, and 3)Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation.The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1)IB4+SNS-Cre/TdTomato+, 2)IB4-SNS-Cre/TdTomato+, and 3)Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation.

opencc-zeroOct 2019View details →

Data from: Single-cell selectivity and functional architecture of human lateral occipital complex

The human lateral occipital complex (LOC) is more strongly activated by images of objects compared to scrambled controls, but detailed information at the neuronal level is currently lacking. We recorded with microelectrode arrays in the LOC of two patients, and obtained highly selective single-unit, multi-unit and high-gamma responses to images of objects. Contrary to predictions derived from functional imaging studies, all neuronal properties indicated that the posterior subsector of LOC we recorded from occupies an unexpectedly high position in the hierarchy of visual areas. Notably, the response latencies of LOC neurons were long, the shape selectivity was spatially clustered, LOC receptive fields were large and bilateral, and a number of LOC neurons exhibited 3D-structure selectivity (a preference for convex or concave stimuli), which are all properties typical of end-stage ventral stream areas. Thus, our results challenge prevailing ideas about the position of the more posterior subsector of LOC in the hierarchy of visual areas.

opencc-by-4.0Apr 2014View details →

Long-Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat Array

Although Schyzosaccharomyces pombe is one of the principal model organisms for studying the cell cycle, surprisingly few methods have characterized S. pombe growth on the single cell level, and no methods exist capable of analyzing thousands of cells and tens of thousands of cell division events. We developed an automated microfluidic platform permitting S. pombe to be grown on-chip for several days under defined and changeable conditions. We developed an image processing pipeline to extract and quantitate several physiological parameters including cell length, time to division, and elongation rate without requiring synchronization of the culture. Over a period of 50 hours our platform analyzed over 100000 cell division events and reconstructed single cell lineages up to 10 generations in length. We characterized cell lengths and division times in a temperature shift experiment in which cells were initially grown at 30°C and transitioned to 25°C. Although cell length was identical at both temperatures at steady-state, we observed transient changes in cell length if the temperature shift took place during a critical phase of the cell cycle. We further show that cells born with normal length do divide over a wide range of cell lengths and that cell length appears to be controlled in the second generation, were large newly born cells have a tendency to divide more rapidly and thus at a normalized cell size. The platform is thus applicable to measure fine-details in cell cycle dynamics, should be a useful tool to decipher the molecular mechanism underlying size homeostasis, and will be generally applicable to study processes on the single cell level that require large numbers of precision measurements and single cell lineages.