keyword
https://read.qxmd.com/read/38540357/single-cell-transcriptomic-profiling-identifies-molecular-phenotypes-of-newborn-human-lung-cells
#1
JOURNAL ARTICLE
Soumyaroop Bhattacharya, Jacquelyn A Myers, Cameron Baker, Minzhe Guo, Soula Danopoulos, Jason R Myers, Gautam Bandyopadhyay, Stephen T Romas, Heidie L Huyck, Ravi S Misra, Jennifer Dutra, Jeanne Holden-Wiltse, Andrew N McDavid, John M Ashton, Denise Al Alam, S Steven Potter, Jeffrey A Whitsett, Yan Xu, Gloria S Pryhuber, Thomas J Mariani
While animal model studies have extensively defined the mechanisms controlling cell diversity in the developing mammalian lung, there exists a significant knowledge gap with regards to late-stage human lung development. The NHLBI Molecular Atlas of Lung Development Program (LungMAP) seeks to fill this gap by creating a structural, cellular and molecular atlas of the human and mouse lung. Transcriptomic profiling at the single-cell level created a cellular atlas of newborn human lungs. Frozen single-cell isolates obtained from two newborn human lungs from the LungMAP Human Tissue Core Biorepository, were captured, and library preparation was completed on the Chromium 10X system...
February 26, 2024: Genes
https://read.qxmd.com/read/38525148/a-chromosome-level-genome-assembly-of-solanum-chilense-a-tomato-wild-relative-associated-with-resistance-to-salinity-and-drought
#2
JOURNAL ARTICLE
Corentin Molitor, Tomasz J Kurowski, Pedro M Fidalgo de Almeida, Zoltan Kevei, Daniel J Spindlow, Steffimol R Chacko Kaitholil, Justice U Iheanyichi, H C Prasanna, Andrew J Thompson, Fady R Mohareb
INTRODUCTION: Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. METHODS: In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38521932/cryopreservation-of-cerebrospinal-fluid-cells-preserves-the-transcriptional-landscape-for-single-cell-analysis
#3
JOURNAL ARTICLE
Mahesh Chandra Kodali, Jerry Antone, Eric Alsop, Rojashree Jayakumar, Khushi Parikh, Aude Chiot, Paula Sanchez-Molina, Bahareh Ajami, Steven E Arnold, Kendall Jensen, Sudeshna Das, Marc S Weinberg
Cerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. the advent of a microfluidics-based multi-omics approach to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses...
March 23, 2024: Journal of Neuroinflammation
https://read.qxmd.com/read/38495503/identification-of-t-cell-exhaustion-related-genes-and-prediction-of-their-immunotherapeutic-role-in-lung-adenocarcinoma
#4
JOURNAL ARTICLE
Chaoqun Lian, Feifan Li, Yiluo Xie, Linxiang Zhang, Huili Chen, Ziqiang Wang, Xinyu Pan, Xiaojing Wang, Jing Zhang
Background: Lung adenocarcinoma ranks as the second most widespread form of cancer globally, accompanied by a significant mortality rate. Several studies have shown that T cell exhaustion is associated with immunotherapy of tumours. Consequently, it is essential to comprehend the possible impact of T cell exhaustion on the tumor microenvironment. The purpose of this research was to create a TEX-based model that would use single-cell RNA-seq (scRNA-seq) and bulk-RNA sequencing to explore new possibilities for assessing the prognosis and immunotherapeutic response of LUAD patients...
2024: Journal of Cancer
https://read.qxmd.com/read/38478395/scpathoquant-a-tool-for-efficient-alignment-and-quantification-of-pathogen-sequence-reads-from-10x-single-cell-sequencing-data-sets
#5
JOURNAL ARTICLE
Leanne S Whitmore, Jennifer Tisoncik-Go, Michael Gale
MOTIVATION: Currently there is a lack of efficient computational pipelines/tools for conducting simultaneous genome mapping of pathogen-derived and host reads from single cell RNA sequencing (scRNAseq) output from pathogen-infected cells. Contemporary options include processes involving multiple steps and/or running multiple computational tools, increasing user operations time. RESULTS: To address the need for new tools to directly map and quantify pathogen and host sequence reads from within an infected cell from scRNAseq data sets in a single operation, we have built a python package, called scPathoQuant...
March 13, 2024: Bioinformatics
https://read.qxmd.com/read/38475481/genome-size-in-the-arenaria-ciliata-species-complex-caryophyllaceae-with-special-focus-on-northern-europe-and-the-arctic
#6
JOURNAL ARTICLE
Gregor Kozlowski, Yann Fragnière, Benoît Clément, Olivier Gilg, Benoît Sittler, Johannes Lang, Pernille Bronken Eidesen, Simone I Lang, Pawel Wasowicz, Conor Meade
The main aim of the present study has been the completion of genome size data for the diverse arctic-alpine A. ciliata species complex, with special focus on the unexplored arctic taxon A. pseudofrigida , the north-European A. norvegica, and A. gothica from Gotland (Sweden). Altogether, 46 individuals of these three Nordic taxa have been sampled from seven different regions and their genome size estimated using flow cytometry. Three other alpine taxa in the A. ciliata complex ( A. multicaulis , A. ciliata subsp...
February 26, 2024: Plants (Basel, Switzerland)
https://read.qxmd.com/read/38472267/single-cell-transcriptomics-of-the-human-parasite-schistosoma-mansoni-first-intra-molluscan-stage-reveals-tentative-tegumental-and-stem-cell-regulators
#7
JOURNAL ARTICLE
Carmen L Diaz Soria, Teresa Attenborough, Zhigang Lu, Santiago Fontenla, Jennie Graham, Christopher Hall, Sam Thompson, Toby G R Andrews, Kate A Rawlinson, Matthew Berriman, Gabriel Rinaldi
Schistosomiasis is a major Neglected Tropical Disease, caused by the infection with blood flukes in the genus Schistosoma. To complete the life cycle, the parasite undergoes asexual and sexual reproduction within an intermediate snail host and a definitive mammalian host, respectively. The intra-molluscan phase provides a critical amplification step that ensures a successful transmission. However, the cellular and molecular mechanisms underlying the development of the intra-molluscan stages remain poorly understood...
March 12, 2024: Scientific Reports
https://read.qxmd.com/read/38464256/defining-the-t-cell-transcriptional-landscape-in-pediatric-liver-transplant-rejection-at-single-cell-resolution
#8
Anna L Peters, Erica A K DePasquale, Gousia Begum, Krishna M Roskin, E Steve Woodle, David A Hildeman
Acute cellular rejection (ACR) affects >80% of pediatric liver transplant recipients within 5 years, and late ACR is associated with graft failure. Traditional anti-rejection therapy for late ACR is ineffective and has remained unchanged for six decades. Although CD8+ T cells promote late ACR, little has been done to define their specificity and gene expression. Here, we used single-cell sequencing and immune repertoire profiling (10X Genomics) on 30 cryopreserved 16G liver biopsies from 14 patients (5 pre-transplant or with no ACR, 9 with ACR)...
February 29, 2024: bioRxiv
https://read.qxmd.com/read/38444087/spatialview-an-interactive-web-application-for-visualization-of-multiple-samples-in-spatial-transcriptomics-experiments
#9
JOURNAL ARTICLE
Chitrasen Mohanty, Aman Prasad, Lingxin Cheng, Lisa M Arkin, Bridget E Shields, Beth Drolet, Christina Kendziorski
MOTIVATION: Spatial transcriptomics (ST) experiments provide spatially localized measurements of genome-wide gene expression allowing for an unprecedented opportunity to investigate cellular heterogeneity and organization within a tissue. Statistical and computational frameworks exist that implement robust methods for pre-processing and analyzing data in ST experiments. However, the lack of an interactive suite of tools for visualizing ST data and results currently limits the full potential of ST experiments...
March 5, 2024: Bioinformatics
https://read.qxmd.com/read/38443925/development-and-proof-of-concept-demonstration-of-a-clinical-metagenomics-method-for-the-rapid-detection-of-bloodstream-infection
#10
JOURNAL ARTICLE
Lluis Moragues-Solanas, Thanh Le-Viet, Elinor McSorley, Carl Halford, Daniel S Lockhart, Alp Aydin, Gemma L Kay, Ngozi Elumogo, William Mullen, Justin O'Grady, Matthew W Gilmour
BACKGROUND: The timely and accurate diagnosis of bloodstream infection (BSI) is critical for patient management. With longstanding challenges for routine blood culture, metagenomics is a promising approach to rapidly provide sequence-based detection and characterisation of bloodborne bacteria. Long-read sequencing technologies have successfully supported the use of clinical metagenomics for syndromes such as respiratory illness, and modified approaches may address two requisite factors for metagenomics to be used as a BSI diagnostic: depletion of the high level of host DNA to then detect the low abundance of microbes in blood...
March 5, 2024: BMC Medical Genomics
https://read.qxmd.com/read/38415934/high-resolution-profiling-of-human-vocal-fold-cellular-landscapes-with-single-nuclei-rna-sequencing
#11
JOURNAL ARTICLE
Benjamin M Laitman, Daniel Charytonowicz, Ashley J Zhu, Katie Lynch, Eleni A Varelas, Madeline Burton, Christina Andreou, Pragati Kore, Diana N Kirke, Ya-Wen Chen, Kristin G Beaumont, Robert Sebra, Eric M Genden, Mark S Courey
INTRODUCTION: The function of the vocal folds (VFs) is determined by the phenotype, abundance, and distribution of differentiated cells within specific microenvironments. Identifying this histologic framework is crucial in understanding laryngeal disease. A paucity of studies investigating VF cellular heterogeneity has been undertaken. Here, we examined the cellular landscape of human VFs by utilizing single-nuclei RNA-sequencing. METHODS: Normal true VF tissue was excised from five patients undergoing pitch elevation surgery...
February 28, 2024: Laryngoscope
https://read.qxmd.com/read/38385967/single-cell-rna-seq-reveals-transcriptomic-modulation-of-alzheimer-s-disease-by-activated-protein-c
#12
JOURNAL ARTICLE
Mohammad Kasim Fatmi, Hao Wang, Lily Slotabec, Changhong Wen, Blaise Seale, Bi Zhao, Ji Li
Single-Cell RNA sequencing reveals changes in cell population in Alzheimer's disease (AD) model 5xFAD (5x Familial AD mutation) versus wild type (WT) mice. The returned sequencing data was processed through the 10x Genomics CellRanger platform to perform alignment and form corresponding matrix to perform bioinformatic analysis. Alterations in glial cells occurred in 5xFAD versus WT, especially increases in microglia proliferation were profound in 5xFAD. Differential expression testing of glial cells in 5xFAD versus WT revealed gene regulation...
February 21, 2024: Aging
https://read.qxmd.com/read/38376487/a-high-quality-blue-whale-genome-segmental-duplications-and-historical-demography
#13
JOURNAL ARTICLE
Yury V Bukhman, Phillip A Morin, Susanne Meyer, Li-Fang Chu, Jeff K Jacobsen, Jessica Antosiewicz-Bourget, Daniel Mamott, Maylie Gonzales, Cara Argus, Jennifer Bolin, Mark E Berres, Olivier Fedrigo, John Steill, Scott A Swanson, Peng Jiang, Arang Rhie, Giulio Formenti, Adam M Phillippy, Robert S Harris, Jonathan M D Wood, Kerstin Howe, Bogdan M Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, J Spencer Johnston, Alexander Ionkov, Kalpana Raja, Huishi Toh, Aimee Lang, Magnus Wolf, Erich D Jarvis, James A Thomson, Mark J P Chaisson, Ron Stewart
The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10X, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl...
February 20, 2024: Molecular Biology and Evolution
https://read.qxmd.com/read/38342952/spatial-transcriptomics-reveals-alterations-in-perivascular-macrophage-lipid-metabolism-in-the-onset-of-wooden-breast-myopathy-in-broiler-chickens
#14
JOURNAL ARTICLE
Ziqing Wang, Paul Khondowe, Erin Brannick, Behnam Abasht
This study aims to use spatial transcriptomics to characterize the cell-type-specific expression profile associated with the microscopic features observed in Wooden Breast myopathy. 1 cm3 muscle sample was dissected from the cranial part of the right pectoralis major muscle from three randomly sampled broiler chickens at 23 days post-hatch and processed with Visium Spatial Gene Expression kits (10X Genomics), followed by high-resolution imaging and sequencing on the Illumina Nextseq 2000 system. WB classification was based on histopathologic features identified...
February 11, 2024: Scientific Reports
https://read.qxmd.com/read/38326333/chromosome-level-genome-assembly-of-the-etruscan-shrew-suncus-etruscus
#15
JOURNAL ARTICLE
Yury V Bukhman, Susanne Meyer, Li-Fang Chu, Linelle Abueg, Jessica Antosiewicz-Bourget, Jennifer Balacco, Michael Brecht, Erica Dinatale, Olivier Fedrigo, Giulio Formenti, Arkarachai Fungtammasan, Swagarika Jaharlal Giri, Michael Hiller, Kerstin Howe, Daisuke Kihara, Daniel Mamott, Jacquelyn Mountcastle, Sarah Pelan, Keon Rabbani, Ying Sims, Alan Tracey, Jonathan M D Wood, Erich D Jarvis, James A Thomson, Mark J P Chaisson, Ron Stewart
Suncus etruscus is one of the world's smallest mammals, with an average body mass of about 2 grams. The Etruscan shrew's small body is accompanied by a very high energy demand and numerous metabolic adaptations. Here we report a chromosome-level genome assembly using PacBio long read sequencing, 10X Genomics linked short reads, optical mapping, and Hi-C linked reads. The assembly is partially phased, with the 2.472 Gbp primary pseudohaplotype and 1.515 Gbp alternate. We manually curated the primary assembly and identified 22 chromosomes, including X and Y sex chromosomes...
February 7, 2024: Scientific Data
https://read.qxmd.com/read/38319079/lack-of-dosage-balance-and-incomplete-dosage-compensation-in-the-zz-zw-gila-monster-heloderma-suspectum-revealed-by-de-novo-genome-assembly
#16
JOURNAL ARTICLE
Timothy H Webster, Annika Vannan, Brendan J Pinto, Grant Denbrock, Matheo Morales, Greer A Dolby, Ian T Fiddes, Dale F DeNardo, Melissa A Wilson
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes...
February 6, 2024: Genome Biology and Evolution
https://read.qxmd.com/read/38314025/association-of-hbsag-levels-with-differential-gene-expression-in-nk-cd8-t-and-memory-b-cells-in-treated-patients-with-chronic-hbv
#17
JOURNAL ARTICLE
Boris J B Beudeker, Zgjim Osmani, Gertine W van Oord, Zwier M A Groothuismink, Robert J de Knegt, Remco M Hoogenboezem, Eric M J Bindels, Harmen J G van de Werken, Andre Boonstra
BACKGROUND & AIMS: HBsAg secretion may impact immune responses to chronic HBV infection. Thus, therapeutic approaches to suppress HBsAg production are being investigated. Our study aims to examine the immunomodulatory effects of high and low levels of circulating HBsAg and thereby improve our understanding of anti-HBV immunity. METHODS: An optimized 10x Genomics single-cell RNA sequencing workflow was applied to blood samples and liver fine-needle aspirates from 18 patients undergoing tenofovir/entecavir (NUC) treatment for chronic HBV infection...
February 2024: JHEP reports: innovation in hepatology
https://read.qxmd.com/read/38311573/characterization-of-the-nucleus-pulposus-progenitor-cells-via-spatial-transcriptomics
#18
JOURNAL ARTICLE
Yu Chen, Long Zhang, Xueqing Shi, Jie Han, Jingyu Chen, Xinya Zhang, Danlin Xie, Zan Li, Xing Niu, Lijie Chen, Chaoyong Yang, Xiujie Sun, Taifeng Zhou, Peiqiang Su, Na Li, Matthew B Greenblatt, Rongqin Ke, Jianming Huang, Zhe-Sheng Chen, Ren Xu
Loss of refreshment in nucleus pulposus (NP) cellularity leads to intervertebral disc (IVD) degeneration. Nevertheless, the cellular sequence of NP cell differentiation remains unclear, although an increasing body of literature has identified markers of NP progenitor cells (NPPCs). Notably, due to their fragility, the physical enrichment of NP-derived cells has limited conventional transcriptomic approaches in multiple studies. To overcome this limitation, a spatially resolved transcriptional atlas of the mouse IVD is generated via the 10x Genomics Visium platform dividing NP spots into two clusters...
February 4, 2024: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://read.qxmd.com/read/38301266/genome-assembly-and-annotation-of-the-mermithid-nematode-mermis-nigrescens
#19
JOURNAL ARTICLE
Upendra R Bhattarai, Robert Poulin, Neil J Gemmell, Eddy Dowle
Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. A lack of genomic resources has limited the expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long-reads and 10X chromium link-reads...
February 1, 2024: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/38293140/single-cell-analysis-reveals-an-antiviral-network-that-controls-zika-virus-infection-in-human-dendritic-cells
#20
Kathryn M Moore, Adam-Nicolas Pelletier, Stacey Lapp, Amanda Metz, Gregory K Tharp, Michelle Lee, Swati Sharma Bhasin, Manoj Bhasin, Rafick-Pierre Sékaly, Steven E Bosinger, Mehul S Suthar
Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10x Genomics Chromium single cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human moDCs infected with ZIKV at the single cell level...
January 21, 2024: bioRxiv
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