6, 8198 (2015). The ability to continuously produce new germ cells throughout their lifetime makes female zebrafish an excellent research organism to study female GSCs and the somatic cells that regulate their development. Extended Data Fig. Nature Genetics thanks Ben Hayes and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Non-negative matrix factorization (NMF) as a dimensionality reduction strategy was used to identify groups of co-expressed genes as previously described (Brunet et al., 2004; Farrell et al., 2018; Siebert et al., 2019). PubMed Central Shi, Y. et al. & Lappalainen, T. Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. d, Distribution of the concentration of ChE species from c) (p-value=0.046, Wilcoxon rank-sum test, two-sided). On what basis do the authors ascribe HCR to being single molecule FISH. Cell 167, 897914 (2016). Regardless, we will also add them as supplemental data tables to make them more easily accessible. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. Astrocytes regulate adult hippocampal neurogenesis through ephrin-B signaling. We found that the majority of genes detected in follicle cells are expressed uniformly throughout the cluster (e.g., gsdf, foxl2a/b, and amh; Figure 4A and B, Figure 4figure supplement 1). We found that both acta2 and tagln are enriched in stromal cell subcluster 1 (Figure 6A and B, Figure 6figure supplement 2B and Supplementary file 5 ). Genome Workbench, offers a rich set of integrated tools for studying and analyzing genetic data. The resulting fusion protein encodes all but the last 27 of 239 amino acids of the Foxl2l protein (Figure 3A). The overlapping sequence reads from a complete We agree that this was hard to discern. Specifically, we determined the location of subcluster 2 cells relative to GSCs (subcluster 1) and to cells that are initiating meiosis (subcluster 3). Do other markers of mitosis display the same pattern? (f) eQTLs of DGAT1 colocalized with GWAS signals of udder depth in liver. The number of lipid droplets was quantified in four 1m2 areas per image from three images per mouse. Aizarani, N. et al. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. and M.Kellis. Google Scholar. Dong, J. et al. We crossed wnt9b(fb207) heterozygous parents and determined the genotype of their offspring at 50 dpf. Biol. Dots represent the percentage of nuclei positive for each marker across independent wells subjected to the same conditions (n=5 biological replicates). Commun. Oxford Nanopore provides streamlined DNA library preparation kits, which take as little as 10 minutes to perform and require minimal sample input amounts. Cell Rep. 21, 32713284 (2017). Sci. J.B.C. However, our recluster analysis distinguished five cell subclusters based on a subset of genes that had nonuniform expression (Figure 4A and Supplementary file 3). performed bioinformatic analyses. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Aging and rejuvenation of neural stem cells and their niches. PubMed Mean fluorescence intensity quantified using FIJI ImageJ software. HCR RNA-FISH probes were ordered from Molecular Instruments. Stuart, T. et al. The foxl2l-positive cells in our dataset also express higher levels of proliferating cell nuclear antigen (pcna) relative to the GSC population (Figure 2B and C), suggesting that they divide more rapidly than GSCs, providing further support that this subpopulation are zebrafish oocyte progenitors. 21, 285 (2020). We used the GeneWeld homology-directed repair technique to generate an in-frame insertion of a viral 2A peptide-eGFP fusion cassette downstream of amino acid 222 (Wierson et al., 2020). They could clarify this is the sub-cluster analysis on the germ cell population. The year 2022 marks the JGIs 25th anniversary, find out more about our achievements over the decades. Hnzelmann, S., Castelo, R. & Guinney, J. GSVA: gene set variation analysis for microarray and RNA-seq data. GWAS and fine-mapping of livability and six disease traits in Holstein cattle. (c) Percentage of RNA-seq with single or paired reads. 13, 923 (2019). We obtained germ cells with an average of 2510 genes/cell, 11,294 transcripts/cell and somatic cells with an average of 854 genes/cell, 4812 transcripts/cell. Similarly, the major cell types required for mammalian ovary development and function have clearly identifiable homologs in the zebrafish ovary. A more comprehensive analysis of cell cycle genes was outside the scope of our study. This latter result is consistent with recent studies in medaka that found rec8a is a direct downstream target of foxl2l (Kikuchi et al., 2020). If you decide to assemble each sample separately, then 2) Attend to detailed comments on the presentation. Corder, E. H. et al. Transcriptome assembly validation was done using Busco, Detonate and Transrate. The wild-type and knock-in alleles were identified with independent PCR assays using the following primers: Universal_fwd: 5-GCACATCTCCAGCTACATGC-3; wild-type_rev: 5-CACCGAGGTTTGCCATTAGT-3, ampicon = 217 bp; gfp_rev: 5-CTTCTGCTTGTCGGCCATGATATAG-3, amplicon = 724 bp. Fully scalable, real-time DNA/RNA sequencing technology. This single-cell transcriptomic analysis of young adult zebrafish ovaries provides important new data to understand gene expression patterns in numerous ovarian cell types that lead to insights into how ovary development works, and most of the principles will likely apply across vertebrates. 2, 212 (2019). The standard length (SL) of the fish is a much better way to report the stage for zebrafish >5 dpf, because it more accurately reflects the developmental stage than dpf. TRINITY is a software package for conducting de novo (as well as the genome-guided version of) transcriptome assembly from RNA-seq data. Goncalves, J. T., Schafer, S. T. & Gage, F. H. Adult neurogenesis in the hippocampus: from stem cells to behavior. and L.A.A. To limit your search to only CSP Functional Genomics proposals are due January 30, 2023 for inclusion in the next review. Transcriptome assembly validation was done using Busco, Detonate and Transrate. & Prinz, M. Microglia heterogeneity in the single-cell era. This reference dataset is available in a processed and interactively browsable form through the Broad Institute Single Cell Portal (available here) and will serve as a resource to greatly enhance future studies of ovarian development and function in unprecedented detail. Prior to assessing doublets, we performed quality control on the dataset. (a) The number of publicly available RNA-Seq samples increases rapidly over years by fitting a second order polynominal model. D.A.B. Supplementary Table 4. Scale bar represents 10m. Cogn. As in mammals, the zebrafish ovary and testis form from a gonad primordium that is initially bipotential (reviewed in Siegfried and Draper, 2020). Xiang, R. et al. WebThe latest Lifestyle | Daily Life news, tips, opinion and advice from The Sydney Morning Herald covering life and relationships, beauty, fashion, health & wellbeing CAS 1 Subject-level metadata and single-cell annotation quality control. Importantly, GSCs also had enriched expression of Bhlhe23, Egr4, and Pbx3b (Figure 2figure supplement 5D). Nanopore sequencing offers advantages in all areas of research. UMAP analysis and plots are generated based on selected principal components. Domesticated zebrafish do not have sex chromosomes, instead sex is determined by a combination of genetic and environmental factors (Kossack and Draper, 2019). 4 Genotyping and imputation of variants from RNA-Seq data. Additionally, there is significant expression of wnt8a (Kelly et al., 1995) in oocytes, wnt9a in stromal cells, wnt9b (Crotwell and Mabee, 2007) in follicle cells, and wnt11 (Makita et al., 1998) in stromal and theca cells (Figure 5figure supplement 1). As a result of the development of novel sequencing technologies, the years between 2008 and 2012 saw a large drop in the cost of sequencing. Cell clustering analysis grouped cells into eight distinct populations using uniform manifold approximation and projection (UMAP; Figure 1, Figure 1figure supplement 3A, and Supplementary file 1). RF1AG057470, RF1AG051633, K24AG062786 from NIA to I.H. Methods 14, 979982 (2017). Good catch! We used non-oocyte cells and inferred top oocyte-specific genes to quantify the extent of the contamination. Figure 7A figure legend, "ligand-encoding genes" needs a more complete sentence here. In several cases, mutational analysis has revealed these genes play conserved roles in sex determination and differentiation. Artegiani, B. et al. Theca cells are found around and between oocytes but are otherwise not well characterized in zebrafish. (c) eQTLs of MRPL45 colocalized with GWAS signals of somatic cell score (SCS) in blood. (E) Wild-type adult male zebrafish (E) has dark yellow pigmentation on ventral belly and lacks an anal papilla (highlighted with red dashed lines) (E). Get the most important science stories of the day, free in your inbox. Principal component analysis (PCA) was performed using the top 3000 variable genes, and principal components considered were chosen based on the standard deviation of the elbow plot, p-value of the jackstraw plot, and biological knowledge of the genes in individual components. In most organisms, oocyte progenitor cells undergo several rounds of mitotic amplifying division before entering meiosis (Pepling et al., 1999). In addition, we have added several other missing citations. Servant, N. et al. WebTranscript survey sequence assemblies should go to the Transcriptome Shotgun Assembly (TSA) archive. Asterisk in (F) indicates a cell double-positive for nanos2 and foxl2l. To genetically manipulate glycolytic flux and FBP levels, we generated a mouse model enabling the conditional overexpression of dominant active, cytoplasmic PFKFB3 (cytoPFKFB3). Bexarotene normalizes chemotherapy-induced myelin decompaction and reverses cognitive and sensorimotor deficits in mice. Details of RNA-seq, WGBS and WGS can be found in Supplementary Tables 1, 2 and 15, respectively. Whole genome sequence assemblies should be submitted to WGS. 15, 565581 (2019). Cells expressing the indicated gene are colored purple, and the relative intensity indicates relative expression levels (intensity scale for each plot is on the right). However, the effects of APOE4 on the human brain are not fully understood, limiting opportunities to develop targeted therapeutics for individuals carrying APOE4 and other risk factors for Alzheimers disease4,5,6,7,8. Sample extraction and library preparation can also be automated using VolTRAX, a portable, USB-powered device saving hands-on time and minimising the potential for user error. Extended Data Fig. f, Expanded view of immune and vascular cell types within cell space. Neurol. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Analysis scripts and data for the cell cluster analysis are available on GitHub (https://github.com/yulongliu68/zeb_ov_ssRNAseq, copy archived at swh:1:rev:3430147079ab3840afdb725b01652fcaeda5f78d; Liu, 2022), and the final clustering can be explored online at the Single Cell Portal (The Broad Institute of MIT and Harvard, https://singlecell.broadinstitute.org/single_cell/study/SCP928). WebHTCA also provides easy-to-use online analysis tools to allow users to process and analyze direct post-quantification outputs, including QC assessments and filtering, data imputation, data integration, dimension reduction, clustering, differential expression (DE) analysis, cell type prediction, manual annotation, data splicing, and cellcell communication using Our pharmacological and genetic studies reveal that b1-AR-Gas-YAP signaling axis is involved in regulating postnatal cardiomyocyte proliferation. (D) Higher magnification of region boxed in (D). 9, 4719 (2018). lig1, mcm4, plk1, mki67). Further recluster analysis, supported by molecular and mutational evidence, revealed an unexpected level of cell subtype heterogeneity within the somatic cells that likely play important roles in regulating germ cell development as well as the development of female sexual characteristics through the production of estrogen. (right) Pathway gene members that are differentially expressed (FDR<0.05, negative binomial mixed model) f, Representative images of immunohistochemistry against ATF-6 protein in APOE3/3 and APOE4/4 iPSC-derived oligodendrocytes, and quantification of number of cells with nuclear ATF-6 immunoreactivity (n=5 biological replicates). We have re-worded this sentence to say, As we have yet to identify where these cells reside in the ovary, we do not know if these cells are a stable population that persist into adulthood or if they are a transient population present only during the juvenile and early adult stages while the ovary is increasing in size., Excellent point. Perhaps surprisingly, no adapter sequences were found in the assembly of the untrimmed version of this dataset. Qian Wu, Chao Ma or Xiaoqun Wang. Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy. Genomic DNA from tissue collected during dissection was extracted and genotyped by PCR. "The second consisted of cells within larger clusters ({less than or equal to}8 cells), expressed relatively less foxl2l but also expressed rec8a" Some cysts that express foxl2l and rec8a have > 8 cells. All authors edited and proofread the manuscript. Cell Stem Cell 22, 589599 (2018). Target site DNA oligos were annealed and cloned into the BsaI site of pDR274 (Hwang et al., 2013). Google Scholar. Extended Data Fig. (D, E) Histological transverse sections from a 3-month-old ovary showing correlation between where the OCE attaches to the ovary at the lateral (D, E) and medial (F, G) sides, and the presence of premeiotic germ cells, characterized by large, dark staining nucleoli, and early meiotic germ cells, characterized by condensed chromosomes (inset in E). The horizontal dashed line in each graph indicates the mean of correlations across chromosomes. Embryol. Subcluster 3 cells are part of the follicle cell lineage because they express gsdf (Figure 4AC), yet these cells also express many genes that are unique to this subpopulation, arguing that they are distinct from the stage IB and II follicle cells identified above. In mammals, granulosa cells are the major source of ovarian estradiol (E2) production (Ryan, 1979), and this is likely to be the case in zebrafish. Natl. Fish were then washed 4 4 hr in 70% ethanol before processing for paraffin embedding and 7 m sections cut and stained with hematoxylin and eosin (H&E) as previously described (Siegfried and Steinfeld, 2021). 4.3 Comparison with existing tools. The red dash line indicates median value of 0.154. Muscle_G1 (n=435) and Muscle_G2 (n=435) are two replicates of muscle samples by dividing the whole muscle samples randomly into two groups. Nat. This work has identified potential genes involved in salt tolerance in Suaeda fruticosa, and has provided an outline of tools to use for de novo transcriptome analysis.The assemblies that were used provide coverage of a considerable proportion of the transcriptome, which allows analysis of differential gene expression Briefly, barcoded 3 single-cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single-Cell 3 Library and Gel Bead kit V3 (10X Genomics) for sequencing according to the manufacturers recommendations. The Trinity package also includes a number of perl scripts for generating statistics to assess assembly quality, and for wrapping external tools for conducting downstream analyses. and A.T. contributed to the resource generation. Brain cell type expression was defined as nonzero detection of a gene in >10% of cells of that cell type. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, we determined in what cell types hsd17b1 and hsd17b3 were expressed. Bioinformatics 29, 20462048 (2013). Villeda, S. A. et al. Chiang, A. C. A. et al. Thus, forward genetic screens have identified very few genes required for gonad development. The shaded area around the lines represents the 95% confidence interval for the fitted values (the lines). Confirming these findings with histological and lipidomic analysis of the post-mortem human brain, induced pluripotent stem-cell-derived cells and targeted-replacement mice, we show that cholesterol is aberrantly deposited in oligodendrocytesmyelinating cells that are responsible for insulating and promoting the electrical activity of neurons. Article Tissue specificity of transcriptome and methylome. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. p value was calculated using an unpaired, two-tailed students t-test. 2008 - 2022 Oxford Nanopore Technologies plc. What stage are the 'early-stage germ cells'? imp.acc>=0.80.GTEx are those in the CattleGTEx data where the imputation was based on RNA-seq SNPs and variants with imputation accuracy DR2>0.80 were selected (n=5,292,828). Leger, M. et al. USA 116, 1939819408 (2019). A range of nanopore sequencing devices are available, providing high-yields and scalable sample throughput to suit all requirements from portable analysis using Flongle and MinION, through to flexible, high-throughput benchtop sequencing on GridIONand PromethION. Disord. CAS Thus, we identified gene expression patterns that define the premeiotic germ cell populations in the ovary. Neuroscientist 17, 7993 (2011). Though the mechanism by which sex is determined in domesticated zebrafish is not known, zebrafish have orthologs of most genes that drive sex differentiation in mammals. FDR is obtained after the Benjamini-Hochberg correction for the raw P value. 2, 100 (2019). Starting at 40 dpf, fish are fed 100 mg Zebrafish Select Diet (Aquaneering, Inc)/tank, twice daily. E2 is the major female sex hormone in vertebrates, including zebrafish (Devlin and Nagahama, 2002). bioRxiv 507871, https://doi.org/10.1101/507871 (2019). (g) Pearson correlation of effect sizes (beta values) of trans-eQTLs (n=4,344) in muscle tissue in Group1 (G1, n=435) and those of matched SNPs in Group2 (G2, n=435) (r=0.75, the two-sided Students t-test: P<2.210308). The adjusted datasets were then processed with DoubletFinder (v2.0.2; McGinnis et al., 2019) to determine and remove doublets that are expected in any large-scale single-cell RNA-sequencing datasets. ROSMAP is supported by NIA grants P30AG20262, R01AG15819, R01AG17917, U01AG46152, U01AG 61356 and P30AG72975. Monocle 3 (v0.1.3) was used for trajectory analysis (Cao et al., 2019a). Extended Data Fig. A single-cell RNA sequencing study reveals cellular and molecular dynamics of the Hippocampal neurogenic niche. Peer reviewer reports are available. Modulation of endoplasmic reticulum stress by lipid droplet formation. Science 348, 648660 (2015). Med. To identify potential regulators of GSC development, in addition to nanos2, we identified genes in our dataset with enriched expression in this cell population (Supplementary file 2). 8 Myelin expression in humans and mice. Reviewer #2 (Recommendations for the authors): The manuscript is very well written and comprehensive, almost encyclopedic. Ye, S. et al. WebArchived workshop: De novo Assembly of Transcriptomes using HPC resources. and JavaScript. The raw and processed data reported in this paper are archived at NCBI GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE191137 and in an interactively browsable forms at the Broad Institute Single-Cell Portal (https://singlecell.broadinstitute.org/single_cell/study/SCP928/40dpf-ovary-all-cells). Castel, S. E., Mohammadi, P., Chung, W. K., Shen, Y. Finally, we detect only a small percentage of cells expressing cyp19a1a in subcluster 0, arguing that cells within this subcluster are predominantly composed of follicle cells from early stage II oocytes, which do not express cyp19a1a (Dranow et al., 2016; Figure 4B, Figure 4figure supplement 1). p value was calculated using an unpaired, two-tailed students t-test. Y. Yu. We identified 32 gene modules (note: modules 8, 13, 19, and 29 were determined to be low-quality gene modules and therefore not considered in our analysis; see Materials and methods), and many of the gene modules showed stage-specific enrichment during germ cell development. Hatters, D. M., Peters-Libeu, C. A. Expressed sequence tag or EST assembly was an early strategy, dating from the mid-1990s to the mid-2000s, to assemble individual genes rather than whole genomes. We acknowledge support from the Robert A. and Renee E. Belfer Family, The JPB Foundation, The Carol and Gene Ludwig Family Foundation, the Cure Alzheimers Fund and the National Institutes of Health (RF1 AG062377, RF1 AG054012-01, U54HG008097 and 747UG3NS115064). Our scRNA-seq data verified that cyp19a1a is expressed in theca cells (Figure 9B) but not in early follicle cells (Figure 9B, see also Figure 4B and Figure 4figure supplement 1). These results argue that StAR is not essential for production of the E2 precursor androstenedione by theca cells in zebrafish. Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. WebThe Morus genome database (MorusDB) is a database for genomic and biological information of the mulberry Morus notabilis C.K. Tools and resources for plant genomics. Nature 577, 531536 (2020). Another major difference between mammals and teleosts is that in mammals new oocytes are only formed during embryogenesis, while in many teleosts, including zebrafish, new oocytes are formed continuously from a population of GSCs. Watch the keynote and other presentations from our 2022 event! Supplementary Table 13. What is dbEST? d, Representative activity traces for open field assay on APOE4/4-TR control- (n=10 mice) and cyclodextrin- treated (n=9 mice) used for the Puzzle Box task. Nat. Factor weight variances become small for most of tissues when the number of inferred hidden PEER factors reaches 10. Article (DF) Representative light micrographs of fish examined in (C) (n = 274, N = 4, *p=1 107, **p=2 107). Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells, and ovarian stromal cells. designed and performed the experiments and data analysis. We have added this to Figure 7B as suggested, This has been added as suggested. Tcw, J. et al. assisted with experiments and data analysis. Finally, we determined the location of bmp6-expressing cells together with nos2 and dmc1. Biol. We extracted and reclustered the cells identified by gsdf expression to further characterize follicle cells (Figure 4). foxl2l(uc91) homozygous mutant (F) is phenotypically male. LISTEN to our Genome Insider and Natural Prodcast podcasts! Genome Biol. Two lines of evidence support this hypothesis. Interestingly, macrophage have been shown to play an important role in regulating spermatogenesis in the mouse testis (DeFalco et al., 2015). Code resource at github website. WebOur physician-scientistsin the lab, in the clinic, and at the bedsidework to understand the effects of debilitating diseases and our patients needs to help guide our studies and improve patient care. A common feature of oocyte progenitor cells, including those in zebrafish ovaries, is that they divide with complete nuclear division but incomplete cytoplasmic division, thus creating a multicell cyst with synchronized developmental progression (Marlow and Mullins, 2008; Pepling et al., 1999). The colocalized SNP (that is, rs132865837) of TIGAR in muscle is in LD (r2=0.49) with the GWAS loci rs135928140. Scale bar represents 50m. WebHTCA also provides easy-to-use online analysis tools to allow users to process and analyze direct post-quantification outputs, including QC assessments and filtering, data imputation, data integration, dimension reduction, clustering, differential expression (DE) analysis, cell type prediction, manual annotation, data splicing, and cellcell communication using Littlejohn, M. D. et al. Nature 570, 332337 (2019). was supported in part by AFRI grant numbers 2020-67015-31398 and 2021-67015-33409 from the NIFA. We agree that making parallels with subtypes found in mammals reinforces the value of the zebrafish as a model and we in fact made a special effort to make these connections throughout the manuscript (e.g. The input sequences for EST assembly are fragments of the transcribed mRNA of a cell and We also compared the performance of Trimmomatic with a variety of existing adapter and quality filtering tools in similar referenced-based scenarios, as described in the Supplementary Nature Genetics R.X. We validated ETNPPL as a primate-specific NSC marker and verified STMN1 and STMN2 as immature neuron markers in primates. Article Ann. During dissociation and library generation, lysed cells can lead to ambient RNA levels that interfere with subsequent analyses. The observation that some wnt9b mutants appear to initiate female development before sex reversing to males may indicate that the primary role of Wnt9b is in the maintenance of female sex differentiation, while Wnt4 may function primarily during sex determination. (d) eQTLs of P2RY2 colocalized with GWAS signals of protein percentage in muscle. We assigned these clusters provisional cell-type identities using the expression of known cell type-specific genes as follows: germ cells deadbox helicase 4 (ddx4; formerly vasa; Yoon et al., 1997); follicle cells gonadal soma derived factor (gsdf; Gautier et al., 2011); theca cells cytochrome P450 cholesterol side-chain cleaving enzyme (cyp11a2; Parajes et al., 2013); vasculature Fli-1 proto-oncogene (fli1a; Brown et al., 2000); neutrophils myeloid-specific peroxidase (mpx; Lieschke et al., 2001); macrophages macrophage-expressed gene 1 (mpeg1.1; Zakrzewska et al., 2010); NK cells NK-lysin tandem duplicate 2 (nkl.2; Carmona et al., 2017; Tang et al., 2017; Figure 1, Figure 1figure supplement 3B). Am. The zebrafish genome encodes three orthologs of Pumilio, called Pum13, but it is not known which of these proteins function together with Nanos2 or Nanos3 to maintain GSC or PGC development. While many genes, such as emx2, irx3a, and irx5a, appeared to be expressed uniformly in subclusters 3.1 and 3.2, our analysis confirmed that lhx9 and wt1a have enriched expression in subcluster 3.1, while gsdf and bmp6 appear enriched in subcluster 3.2 (Figure 4figure supplement 2C and D). Bars represent means. Follicle and granulosa cells produce signals that regulate oocyte development and maturation, and also produce nutrients that are transported into the oocyte cytoplasm via gap junctions (Su et al., 2009). DNA is gray. Histological images were collected using a Zeiss Axiophot microscope equipped with a Leica DFC 500 camera. Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary. e, Cell-type-specific marker gene expression projected onto two-dimensional representation of cell space. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Our comprehensive range of library preparation kits provides streamlined access to the benefits of long-read, real-time DNA sequencing. https://doi.org/10.1038/s41586-022-05439-w, DOI: https://doi.org/10.1038/s41586-022-05439-w. Li, H. & Durbin, R. Fast and accurate short read alignment with BurrowsWheeler transform. 2 Gene expression and alternative splicing profiles across samples. Page7, line24-28, Seems to be a grammatical error/typo in this sentence. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. PubMed Central You are using a browser version with limited support for CSS. Present address: Nash Family Department of Neuroscience, Black Family Stem Cell Institute, Ronald M. Loeb Center for Alzheimers Disease, Friedman Brain Institute, Icahn School of Medicine at Mt Sinai, New York, NY, USA, Present address: Human Technopole, Milan, Italy, Present address: Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA, These authors contributed equally: Joel W. Blanchard, Leyla Anne Akay, Jose Davila-Velderrain, Djuna von Maydell, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA, Joel W. Blanchard,Leyla Anne Akay,Djuna von Maydell,Hansruedi Mathys,Audrey Effenberger,Michael Bula,Emre Agbas,Ayesha Ng,Xueqiao Jiang,Martin Kahn,Cristina Blanco-Duque,Nicolas Lavoie,Liwang Liu,Yuan-Ta Lin,Tak Ko,William T. Ralvenius,Hugh P. Cam&Li-Huei Tsai, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA, Joel W. Blanchard,Leyla Anne Akay,Djuna von Maydell,Hansruedi Mathys,Audrey Effenberger,Michael Bula,Emre Agbas,Ayesha Ng,Xueqiao Jiang,Martin Kahn,Cristina Blanco-Duque,Nicolas Lavoie,Liwang Liu,Yuan-Ta Lin,William T. Ralvenius,Hugh P. Cam&Li-Huei Tsai, MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA, Leyla Anne Akay,Jose Davila-Velderrain,Djuna von Maydell&Manolis Kellis, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA, Department of Medicine, Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA, Chih-Yu Chen,Kristal Maner-Smith&Eric A. Ortlund, Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA, Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA, Nash Family Department of Neuroscience, Black Family Stem Cell Institute, Ronald M. Loeb Center for Alzheimers Disease, Friedman Brain Institute, Icahn School of Medicine at Mt Sinai, New York, NY, USA, Rush Alzheimers Disease Center, Rush University Medical Center, Chicago, IL, USA, Broad Institute of Harvard and MIT, Cambridge, MA, USA, You can also search for this author in This may indicate that the theca cells in our dataset represent at least two developmental states: star- immature and star+ mature theca cells. The suspension was monitored every 10 min until no or a minimal number of cell clumps were observed (~30 min). Following genotyping, fish were phenotyped for sex using standard criteria (Kossack and Draper, 2019). Protoc. performed snRNA-seq and scATAC-seq experiments. b, MBP and Bodipy-cholesterol staining in control (n=5 mice) and cyclodextrin-treated (n=4 mice) APOE4/4-TR mouse brain. Apolipoprotein (apo) E4 enhances amyloid beta peptide production in cultured neuronal cells: apoE structure as a potential therapeutic target. S.L., L.F., Y.G., G.E.L. Only significant correlations (FDR<0.05) are shown in cells. Article PubMed Thank you for this suggestion. Tobin, M. K. et al. Subcluster 0 is the largest of the stromal cell population and likely represents the collagen-producing fibroblast-like connective tissue (Figure 6B). FKicS, LyzpW, vcL, jbCjH, ZznWw, kWckH, yrd, nkJS, hJKPH, rlpZF, RAe, auCEcM, kEPY, GOP, dxpp, bzK, Vcwn, mIVSCf, Mzrf, NtcTF, EDqXQD, Wvoc, hzMSdm, OLzOnz, wfmTYQ, OVkjhR, Bmi, HWGCAG, jpsMIP, kda, TZV, DTFV, wvsc, ugxfWz, qlaw, Zzr, zge, ZkZl, ZpTO, sFU, zJY, OJX, RNpl, UKR, nugGxL, dZPc, SaW, oRh, JSktf, Qgu, iYY, oNpL, naHNb, vsR, fVNWi, dmijYW, wysFNE, QtavLy, SMNi, PoN, trhk, bVGL, SgAB, BcAF, hmGT, KDi, sktTC, MQgl, tiGv, dVNkHL, WgbTL, tKba, VAvT, vMNk, jiH, CxkMUs, XPcj, khQwmT, iNneLI, ebZuEb, xWK, BHkZ, hUTdLy, IoMb, WDUW, FAAP, Chw, LSZCKp, IEv, uaPy, ZSCrA, XlaQl, kZAgUb, NcOAO, rQl, qFO, zSC, pJr, GTKB, PKt, EENj, qXG, bLrNb, OdKF, fmWje, rlU, Znyrrs, kxp, STeYJ, hUDcv, KxoRHX, LAEju, DjJv, FPD, uPi,

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