Homo sapiens
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PROVIDER: PRJNA382642 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: To investigate the transcriptomes of H9 human embryonic stem cells (hESCs)- and peripheral blood mononuclear cells (PBMC) originated induced pluripotent stem cells (iPSCs)-derived early stage lentoid bodies at day 24 through RNA-Seq based whole transcriptome sequencing. Methods: The PBMC obtained from a healthy donor were subjected to generate iPSCs using Sendai-virus delivery system Cytotune 2.0 whereas the H9 hESCs were obtained commercially. Both hESCs and iPSCs were differentiated into lentoid bodies using “fried egg” method with feeder-free conditions as described previously. The differentiating lentoid bodies were examined for the expression of lens-specific and pluripotency markers at days 0, 6, 10, 15 and 24 by quantitative real-time PCR (qRT-PCR). Briefly, four biological replicates for each hESCs- and iPSC-derived lentoid bodies at day 24 were used for the RNA-Seq library preparation followed by sequencing on a single lane of HiSeq 2500. The raw reads were processed and analyzed using Lasergene Genomics Suite and the expression profiles were examined for differential expression using Spotfire DecisionSite with Functional Genomics. Results: The differentiating lentoid bodies at day 24 revealed transparent lens like morphological features with an increased expression of lens-specific markers including CRYGC. A total of 193.41, and 170.00 million reads were obtained for hESCs- and iPSCs-derived lentoid bodies, respectively. Of these, >96% reads aligned to the human reference genome resulting in >200x sequence coverage for both hESCs- and iPSCs-derived lentoid bodies. Additional analysis identified expression (≥ 0.659 RPKM) of 13,991 and 14,018 genes in hESCs- and iPSCs-derived lentoid bodies, respectively, representing ~70% of the total human protein-coding transcriptome expressed in lentoid bodies. Finally, a comparative analysis of both hESCs- and iPSCs-derived lentoid bodies transcriptomes identified >96% similarity at the gene level. Conclusion: The transcriptome analysis revealed an overall similar transcriptional profile in both hESCs- and iPSCs-derived lentoid bodies during differentiation at day 24.
2019-12-17 | GSE111071 | GEO
Project description:Differentiation of pluripotent cells to generate lentoid bodies is important for the understanding of the lens development and investigating the processes critical for lens morphogenesis. This Study was initiated to investigate a comprehensive proteome profiling of the peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cell (iPSC)-derived lentoid bodies through mass spectrometry-based protein sequencing. Briefly, a small aliquot of blood sample was ascertained to collect PBMCs that were reprogrammed to iPSCs using the Sendai-virus delivery system. The PBMC-originated, iPSCs were differentiated into lentoid bodies employing the “fried egg” method using feeder-free conditions. The quantitative real-time PCR (qRT-PCR) confirmed the expression of lens-associated markers, which exhibited at least an order magnitude increased expression in lentoid bodies at differentiation day 25. Subsequently, the total cellular protein was extracted from lentoid bodies at day 25, digested with trypsin, fractionated into 24 fractions and subjected to an mass spectrometry-based label-free quantitative proteomics. mass spectrometry-based proteome profiling revealed 9,473 proteins in iPSC-derived lentoid bodies at differentiation day 25. In here, we report a comprehensive proteome of PBMC-originated, iPSC-derived lentoid bodies at day 25, which will help in better understanding processes critical for the development of the ocular lens.
2022-03-01 | PXD011143 | Pride
Project description:Differentiation of pluripotent stem cells into lentoid bodies is important for the understanding of the lens development and investigating the processes critical for lens morphogenesis. This Study was initiated to investigate a comprehensive proteome profiling of the peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cell (iPSC)-derived lentoid bodies through mass spectrometry-based protein sequencing. Briefly, a small aliquot of blood sample was ascertained to collect PBMCs that were reprogrammed to iPSCs using the Sendai-virus delivery system. The PBMC-originated, iPSCs were differentiated into lentoid bodies employing the “fried egg” method using feeder-free conditions. The quantitative real-time PCR (qRT-PCR) confirmed the expression of lens-associated markers, which exhibited at least an order magnitude increased expression in lentoid bodies at differentiation day 35. Subsequently, the total cellular protein was extracted from lentoid bodies at day 35, digested with trypsin, fractionated into 96 fractions and subjected to an mass spectrometry-based label-free quantitative proteomics. mass spectrometry-based proteome profiling revealed 9,717 proteins in iPSC-derived lentoid bodies at differentiation day 35. In here, we report a comprehensive proteome of PBMC-originated, iPSC-derived lentoid bodies at day 35, which will help in better understanding processes critical for the development of the ocular lens.
2022-02-28 | PXD009633 | Pride
Project description:Comparative Transcriptome analysis of hESCs- and iPSCs-derived lentoid body
| PRJNA435838 | ENA
Project description:Long noncoding RNAs (lncRNAs) have emerged as crucial regulators of gene expression during embryonic stem cell (ESC) self-renewal and differentiation. Here, we systemically analyzed the differentially regulated lncRNAs during ESC-derived cardiomyocyte (CM) differentiation. We established a perspicuous profile of lncRNA expression at four critical developmental stages and found that the differentially expressed lncRNAs were grouped into six distinct clusters. The cluster with specific expression in ESC enriches the largest number of lncRNAs. Investigation of lncRNA-protein interaction network revealed that they are not only controlled by classic key transcription factors, but also modulated by epigenetic and epitranscriptomic factors including N6-methyladenosine (m6A) effector machineries.
2022-03-01 | GSE197205 | GEO
Project description:Long noncoding RNAs (lncRNAs) have been implicated in controlling various aspects of embryonic stem cell (ESC) biology, although the functions of specific lncRNAs, and the molecular mechanisms through which they act, remain unclear. Here, we demonstrate discrete and opposing roles for the lncRNA transcript Haunt and its genomic locus in regulating the HOXA gene cluster during ESC differentiation. Reducing or enhancing Haunt expression, with minimal disruption of the Haunt locus, led to up- or down-regulation of HOXA genes, respectively. In contrast, increasingly large genomic deletions within the Haunt locus attenuated HOXA activation. The Haunt DNA locus contains potential enhancers of HOXA activation, whereas Haunt RNA acts to prevent aberrant HOXA expression. This work reveals a multi-faceted model of lncRNA-mediated transcriptional regulation of the HOXA cluster, with distinct roles for a lncRNA transcript and its genomic locus, while illustrating the power of rapid CRISPR/Cas9-based genome editing for assigning lncRNA functions. All RNA-seq(s) were designed to reveal the differentially expressed genes among different stages of ESCs differentiation, or differentially expressed genes between wild-type or Haunt or HOXA mutant cells during RA-induced differentiation. All ChIRP-Seq were used to reveal the DNA or RNA targets of Haunt before or after RA treatment.
2015-04-20 | E-GEOD-58514 | biostudies-arrayexpress
Project description:Vascular smooth muscle cells (SMCs) change between a contractile-differentiated and a proliferative-dedifferentiated phenotype in response to environmental cues. Long non-coding RNAs (lncRNAs) and N6-methyladenosine (m6A) modification regulate cell fate decision. Here we used primary human pulmonary artery SMCs (hPASMCs) and assessed the expression of lncRNAs during SMCs phenotypic modulation. A lncRNA, which we refer to as Differentiation And Growth Arrest-related lncRNA (DAGAR) was increased during differentiation and we demonstrate that it is required for this process. DAGAR was m6A-modified and regulated by the m6A reader YTHDF2 in SMCs and MRC5 cells. A marked downregulation of YTHDF1-3 proteins during both SMC differentiation and MRC5 quiescence was found, consistent with the increase of DAGAR. Remarkably, YTHDF2 immunoprecipitation followed by RNA deep sequencing (RIP-Seq) displayed an enrichment of key SMC-associated transcripts, including smooth muscle myosin heavy chain (MYH11) and members of the TGF, PDGF and VEGF pathways. Knockdown of YTHDF2 induced DAGAR and SMC marker gene expression. We conclude that the lncRNA DAGAR and YTHDF2 contribute to the regulation of SMC plasticity and differentiation programs.
2025-05-06 | PXD029550 | Pride
Project description:Long noncoding RNA (lncRNA) plays important roles in morphological differentiation and development in eukaryotes. In filamentous fungi, however, little is known about lncRNAs and their roles in sexual development. Here we describe sexual stage-induced lncRNAs during the formation of perithecium, the sexual fruiting body of Fusarium graminearum. We identified 547 lncRNAs whose expression were developmental stage-specific; about 40% of them peaked during ascus development, when meiosis occurs. A large fraction of the lncRNAs were found to be antisense to mRNAs, forming 300 sense–antisense pairs. Although small RNAs were produced from these overlapped loci, most of the antisense lncRNAs appeared not to be involved in gene silencing pathways. Rather, the expression of antisense lncRNA and sense mRNA pairs tended to be induced in parallel as the perithecium matured. To identify regulatory components for lncRNA expression, we analyzed mutants defective in the nonsense-mediated decay (NMD) pathway. A subset of lncRNAs was specifically targeted by NMD, suggesting a suppressive role of NMD in lncRNA expression during vegetative growth. This study provides comprehensive resources for studying developmental lncRNA that may be important for laying out the multicellular fruiting body plan.
2018-08-16 | GSE109094 | GEO
Project description:Long noncoding RNA (lncRNA) plays important roles in morphological differentiation and development in eukaryotes. In filamentous fungi, however, little is known about lncRNAs and their roles in sexual development. Here we describe sexual stage-induced lncRNAs during the formation of perithecium, the sexual fruiting body of Fusarium graminearum. We identified 547 lncRNAs whose expression were developmental stage-specific; about 40% of them peaked during ascus development, when meiosis occurs. A large fraction of the lncRNAs were found to be antisense to mRNAs, forming 300 sense–antisense pairs. Although small RNAs were produced from these overlapped loci, most of the antisense lncRNAs appeared not to be involved in gene silencing pathways. Rather, the expression of antisense lncRNA and sense mRNA pairs tended to be induced in parallel as the perithecium matured. To identify regulatory components for lncRNA expression, we analyzed mutants defective in the nonsense-mediated decay (NMD) pathway. A subset of lncRNAs was specifically targeted by NMD, suggesting a suppressive role of NMD in lncRNA expression during vegetative growth. This study provides comprehensive resources for studying developmental lncRNA that may be important for laying out the multicellular fruiting body plan.
2018-08-16 | GSE109088 | GEO
Project description:To investigate expression profile and potential role of lncRNAs in osteogenic differentiation of human adipose-derived stem cells (ASCs), whole genome lncRNA microarray was employed to identify lncRNAs that differentially expressed during osteogenesis of ASCs. Four individual human ASCs derived from four different donors were induced to differentiate into osteoblast in vitro. Expression profiles of lncRNAs and mRNAs of undifferentiated and osteogenic differentiated ASCs were obtained by microarray and compared. The genes that meet both fold change ≥2.0 and p<0.05 were considered as differentially expressed genes during osteogenic differentiation of human ASCs. Expression of five upregulated lncRNAs (SAA3P, LOC284080, XLOC_001453, XLOC_011980, HHIP-AS1) and five downregulated lncRNAs (XLOC_007489, CTC-564N23.3, XLOC_010397, XLOC_002619, LINC00638) from the microarray were quantified in the same RNA samples by real-time PCR, validating the microarray data.
2017-11-01 | GSE89330 | GEO