Comparative transcriptomic analysis of hematopoietic system between human and mouse by Microwell-seq.
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ABSTRACT:
SUBMITTER: Lai S
PROVIDER: S-EPMC6028447 | biostudies-literature | 2018
REPOSITORIES: biostudies-literature
Publications
Comparative transcriptomic analysis of hematopoietic system between human and mouse by Microwell-seq.
Lai Shujing S Huang Wentao W Xu Yang Y Jiang Mengmeng M Chen Haide H Cheng Chen C Lu Yingru Y Huang He H Guo Guoji G Han Xiaoping X
Cell discovery 20180703
Similar Datasets
Project description:Traditional single-cell RNA-seq technologies have shown limitations for large scale experiments. Here, we constructed a single-cell resolution transcriptomic atlas of (HSPCs) in human and mouse,including a total number of 71,729 single cells clustered into 39 subpopulations by computational analysis. In human, we found 20 progenitors primed with unique lineages like megakaryocyte, neutrophil and B cell progenitor can project directly from HSPCs. Within the c-Kit positive cells from mouse bone marrow, we described 19 progenitor subgroups at single cell resolution.
2018-05-18 | GSE92274 | GEO
Project description:(1) Background: mouse models are fundamental to the study of hematopoiesis, but comparisons between mouse and human in single cells have been limited in depth. (2) Methods: we constructed a single-cell resolution transcriptomic atlas of hematopoietic stem and progenitor cells (HSPCs) of human and mouse, from a total of 32,805 single cells. We used Monocle to examine the trajectories of hematopoietic differentiation, and SCENIC to analyze gene networks underlying hematopoiesis. (3) Results: After alignment with Seurat 2, the cells of mouse and human could be separated by same cell type categories. Cells were grouped into 17 subpopulations; cluster-specific genes were species-conserved and shared functional themes. The clustering dendrogram indicated that cell types were highly conserved between human and mouse. A visualization of the Monocle results provided an intuitive representation of HSPC differentiation to three dominant branches (Erythroid/megakaryocytic, Myeloid, and Lymphoid), derived directly from the hematopoietic stem cell and the long-term hematopoietic stem cells in both human and mouse. Gene regulation was similarly conserved, reflected by comparable transcriptional factors and regulatory sequence motifs in subpopulations of cells. (4) Conclusions: our analysis has confirmed evolutionary conservation in the hematopoietic systems of mouse and human, extending to cell types, gene expression and regulatory elements.
| S-EPMC8143332 | biostudies-literature
Project description:Comparative Transcriptomic Analysis of Hematopoietic System Across Species by Microwell-Seq
| PRJNA357074 | ENA
Project description:BackgroundBud dormancy is an important biological phenomenon of perennial plants that enables them to survive under harsh environmental circumstances. Grape (Vitis vinifera) is one of the most grown fruit crop worldwide; however, underlying mechanisms involved in grape bud dormancy are not yet clear. This work was aimed to explore the underlying molecular mechanism regulating bud dormancy in grape.ResultsWe have performed transcriptome and differential transcript expression analyses of "Shine Muscat" grape buds using the Illumina RNA-seq system. Comparisons of transcript expression levels among three stages of dormancy, paradormancy (PD) vs endodormancy (ED), summer buds (SB) vs ED and SB vs PD, resulted in the detection of 8949, 9780 and 3938 differentially expressed transcripts, respectively. Out of approximately 78 million high-quality generated reads, 6096 transcripts were differentially expressed (log2 ratio ≥ 1, FDR ≤ 0.001). Grape reference genome was used for alignment of sequence reads and to measure the expression level of transcripts. Furthermore, findings obtained were then compared using two different databases; Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), to annotate the transcript descriptions and to assign a pathway to each transcript. KEGG analysis revealed that secondary metabolites biosynthesis and plant hormone signaling was found most enriched out of the 127 total pathways. In the comparisons of the PD vs ED and SB vs ED stages of grape buds, the gibberellin (GA) and abscisic acid (ABA) pathways were found to be the most enriched. The ABA and GA pathways were further analyzed to observe the expression pattern of differentially expressed transcripts. Transcripts related to the PP2C family (ABA pathway) were found to be up-regulated in the PD vs ED comparison and down-regulated in the SB vs ED and SB vs PD comparisons. GID1 family transcripts (GA pathway) were up-regulated while DELLA family transcripts were down-regulated during the three dormancy stages. Differentially expressed transcripts (DEGs) related to redox activity were abundant in the GO biological process category. RT-qPCR assay results for 12 selected transcripts validated the data obtained by RNA-seq.ConclusionAt this stage, taking into account the results obtained so far, it is possible to put forward a hypothesis for the molecular mechanism underlying grape bud dormancy, which may pave the way for ultimate improvements in the grape industry.
| S-EPMC5244717 | biostudies-literature
Project description:The aim of the present study was to perform comparative genomics using gene expression profile datasets of mice and humans who had been treated with anticancer drugs, to determine the similarities and differences in the antitumor mechanisms in the two mammals. This involved data mining of antitumor gene expression regulation, and screening of genetic loci from experimental mouse models of antitumor targets, to provide a theoretical basis of drug design. Subsequently, 9 overlapping genes with opposite expression patterns were identified across mouse and human cell lines that were treated with a specific cyclin‑dependent kinase 4/6 inhibitor, PD0332991. These genes included LIM homeobox 2, adenomedullin, bone marrow stromal cell antigen 1, caveolin 1, histone cluster 1 (HIST1) H2B family member C, HIST1 H3 family member F, low density lipoprotein‑receptor related protein 11, prolyl 4‑hydroxylase subunit α1 and torsin family 3 member A. In addition, the janus kinase‑signal transducer and activator of transcription signaling pathway, Toll‑like receptor signaling pathway, T cell receptor signaling pathway and the nucleotide‑binding oligomerization domain‑like receptor signaling pathway were identified as candidate pathways for explaining antitumor mechanisms.
| S-EPMC5647007 | biostudies-literature
Project description:Alterations in multiple subregions of the human prefrontal cortex (PFC) have been heavily implicated in psychiatric diseases. Moreover, emerging evidence suggests that circadian rhythms in gene expression are present across the brain, including in the PFC, and that these rhythms are altered in disease. However, investigation into the potential circadian mechanisms underlying these diseases in animal models must contend with the fact that the human PFC is highly evolved and specialized relative to that of rodents. Here, we use RNA sequencing to lay the groundwork for translational studies of molecular rhythms through a sex-specific, cross species comparison of transcriptomic rhythms between the mouse medial PFC (mPFC) and two subregions of the human PFC, the anterior cingulate cortex (ACC) and the dorsolateral PFC (DLPFC). We find that while circadian rhythm signaling is conserved across species and subregions, there is a phase shift in the expression of core clock genes between the mouse mPFC and human PFC subregions that differs by sex. Furthermore, we find that the identity of rhythmic transcripts is largely unique between the mouse mPFC and human PFC subregions, with the most overlap (20%, 236 transcripts) between the mouse mPFC and the human ACC in females. Nevertheless, we find that basic biological processes are enriched for rhythmic transcripts across species, with key differences between regions and sexes. Together, this work highlights both the evolutionary conservation of transcriptomic rhythms and the advancement of the human PFC, underscoring the importance of considering cross-species differences when using animal models.
| S-EPMC11463408 | biostudies-literature
Project description:IntroductionAlterations in multiple subregions of the human prefrontal cortex (PFC) have been heavily implicated in psychiatric diseases. Moreover, emerging evidence suggests that circadian rhythms in gene expression are present across the brain, including in the PFC, and that these rhythms are altered in disease. However, investigation into the potential circadian mechanisms underlying these diseases in animal models must contend with the fact that the human PFC is highly evolved and specialized relative to that of rodents.MethodsHere, we use RNA sequencing to lay the groundwork for translational studies of molecular rhythms through a sex-specific, cross species comparison of transcriptomic rhythms between the mouse medial PFC (mPFC) and two subregions of the human PFC, the anterior cingulate cortex (ACC) and the dorsolateral PFC (DLPFC).ResultsWe find that while circadian rhythm signaling is conserved across species and subregions, there is a phase shift in the expression of core clock genes between the mouse mPFC and human PFC subregions that differs by sex. Furthermore, we find that the identity of rhythmic transcripts is largely unique between the mouse mPFC and human PFC subregions, with the most overlap (20%, 236 transcripts) between the mouse mPFC and the human ACC in females. Nevertheless, we find that basic biological processes are enriched for rhythmic transcripts across species, with key differences between regions and sexes.DiscussionTogether, this work highlights both the evolutionary conservation of transcriptomic rhythms and the advancement of the human PFC, underscoring the importance of considering cross-species differences when using animal models.
| S-EPMC11769989 | biostudies-literature
Project description:BackgroundSpinal Muscular Atrophy (SMA), a neuromuscular disorder that leads to weakness in the muscles due to degeneration of motor neurons. Mutations in the survival motor neuron 1 (SMN1) gene leads to the deficiency of SMN protein that causes SMA. The molecular alterations associated with SMA extends across the transcriptome and proteome. Although several studies have examined the transcriptomic profile of SMA, the difference in experimental settings across these studies highlight the need for a comparative meta-analysis to better understand these differences.Methods and dataWe conducted a systematic comparative meta-analysis of publicly available gene expression data from six selected studies to elucidate variations in the transcriptomic landscape across different experimental conditions, including tissue types and mouse models. We used both microarray and RNA-seq datasets, retrieved from Gene Expression Omnibus (GEO) and ArrayExpress (AE). Methods included normalization, differential expression analysis, gene-set enrichment analysis (GSEA), network reconstruction and co-expression analysis.ResultsDifferential expression analysis revealed varying numbers of differentially expressed genes ranging between zero and 1,655 across the selected studies. Notably, the Metallothionein gene Mt2 was common in several of the eight comparisons. This highlights its role in oxidative stress and detoxification. Additionally, genes such as Hspb1, St14 and Sult1a1 were among the top ten differentially expressed genes in more than one comparison. The Snrpa1 gene, involved in pre-mRNA splicing, was upregulated in the spinal cord and has a strong correlation with other differentially expressed genes from other comparisons in our network reconstruction analysis. Gene-set enrichment analysis identified significant GO terms such as contractile fibers and myosin complexes in more than one comparison which highlights its significant role in SMA.ConclusionsOur comparative meta-analysis identified only few genes and pathways that were consistently dysregulated in SMA across different tissues and experimental settings. Conversely, many genes and pathways appeared to play a tissue-specific role in SMA. In comparison with the original studies, reproducibility was rather weak.
| S-EPMC11555813 | biostudies-literature
Project description:Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that human and Drosophila cells release similar EVs with diameters ranging from 30 to 200 nm, which contain complex populations of transcripts. RNA-seq identified abundant ribosomal RNAs, related pseudogenes and retrotransposons in human and Drosophila EVs. Vault RNAs and Y RNAs abounded in human samples, whereas small nucleolar RNAs involved in pseudouridylation were most prevalent in Drosophila EVs. Numerous mRNAs were identified, largely consisting of exonic sequences displaying full-length read coverage and enriched for translation and electronic transport chain functions. By analogy with human systems, these sizeable similarities suggest that EVs could potentially enable RNA-mediated intercellular communication in Drosophila.
| S-EPMC4901365 | biostudies-literature
Project description:Tumefactive demyelinating lesion (TDL) is an immune-mediated disease which can be misdiagnosed as glioma. At present, there is no study comparing difference between the two disorders at the cellular level. Here, we perform integrative and comparative single-cell RNA sequencing (ScRNA-seq) transcriptomic analysis on TDL and glioma lesions. At single-cell resolution, TDL is comprised primarily of immune cells, which is completely different from glioma. The integrated analysis reveals a TDL-specific microglial subset involving in B cell activation and proliferation. Comparative analysis highlights remyelination function of glial cells and demyelination function of T cells in TDL. Subclustering and pseudotime trajectory analysis of T cells in TDL reveal their heterogeneity and diverse functions involving in TDL pathogenesis and recovery process. Our study identifies substantial differences between TDL and glioma at single-cell resolution. The observed heterogeneity and potentially diverse functions of cells in TDL may be critical in disease progression.
| S-EPMC9463163 | biostudies-literature