RNA sequencing analyses of wild-type and variant 1q human pluripotent stem cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Homo sapiens
SUBMITTER: Christopher Price
PROVIDER: E-MTAB-13383 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The objective of this study was to determine if a subset of regulatory T cells (Tregs) expressing the transcription factor, Zbtb20, played a unique role in the function of the immune system. Genetic reporter mice were used to isolate Zbtb20-expressing Tregs as well as activated (CD62Llo) and naive (CD62Lhi) Tregs. The gene expression in these cells was determined with RNA-seq.
2022-02-25 | E-MTAB-11442 | biostudies-arrayexpress
Project description:Fibrotic changes in the myocardium and cardiac arrhythmias represent fatal complications in rheumatic disease systemic sclerosis (SSc), however the underlying mechanisms remain elusive. Fos-related antigen-2 (Fosl-2) has been implicated in development of organ fibrosis. Mice overexpressing Fosl-2 (Fosl-2tg) showed interstitial cardiac fibrosis, disorganized connexin43/40 in intercalated discs and deregulated expression of genes controlling conduction system. Fosl-2tg mice developed higher heart rate (HR), prolonged QT intervals, arrhythmias with prevalence of premature ventricular contractions, ventricular tachycardias, II-degree atrio-ventricular blocks and reduced HR variability. Following stimulation with isoproterenol Fosl-2tg mice showed impaired HR response. To assess the role of inflammation in cardiac fibrosis we used Rag2-/-Fosl-2tg mice lacking T/B cells. These mice showed no myocardial fibrosis and ECG abnormalities. Transcriptomics analysis of cardiac Rag-2-/-Fosl-2wt/Rag2-/-Fosl-2tg/Fosl-2tg fibroblasts revealed that systemic inflammation triggered fibrotic and arrhythmogenic alterations while Fosl-2-overexpression mediated profibrotic signature. In human cardiac fibroblasts FOSL-2-overexpression enhanced myofibroblast signature under proinflammatory or profibrotic stimuli. These results demonstrate that under immunofibrotic conditions activator protein 1 transcription factor component Fosl-2 exaggerates myocardial fibrosis, arrhythmias and aberrant response to stress.
2022-10-27 | E-MTAB-12271 | biostudies-arrayexpress
Project description:Lymphedema (LD) is characterized by the accumulation of protein-rich interstitial fluid, lipids and a significant inflammatory cell infiltrate in the limb. It causes a significant morbidity and is a common disabling disease affecting more than 150 million people worldwide, however there is no yet curative treatment. In this study, we found that LD tissues from patients exhibit inflamed gene expression profile compared to their normal arm. This was next confirmed by a lipidomic analysis that revealed severe decrease in arachidonic acid-derived lipid mediators generated by the 15-lipoxygenase (15-LO) in lymphedematous arms. Using a mouse model of lymphedema, we reproduced the etiology of the human pathology including the loss of specialized pro-resolving lipid mediators that play essential role in resolution of inflammation. This was associated with a lack of nonlymphoid PPAR-positive regulatory T cells (Treg) recruitment in the injured limb adipose tissue. Importantly, we identified the lymphatic endothelial 15-LO as responsible for the chemoattraction and survival of this Treg subpopulation. These results were confirmed by an aggravation of LD and degradation of the lymphatic network in an original transgenic mouse model in which ALOX15 gene has been selectively deleted in the lymphatic system (ALOX15lecKO). Importantly, this phenotype was rescued by the injection of ALOX15-expressing lentivectors. These results provide evidence that lymphatic 15-LO may represent a novel therapeutic target for LD by serving as a mediator of nonlymphoid Treg cell population invasion into lymphedematous adipose tissue to resolve inflammation. Experimental workflow: To broadly identify gene expression signatures associated to secondary LD, we performed bulk-RNA sequencing on dermolipectomy tissue samples from women who developed LD after breast cancer. Four patient biopsies (normal arm and LD arm in each patient) were studied and the differential expression analysis (DEseq) followed by a protein-coding RNA profiling.
2023-06-09 | E-MTAB-13019 | biostudies-arrayexpress
Project description:The transcriptomic innate immune response derived from human nasal epithelial cells depends on how Streptococcus pneumoniae colonises the nasopharynx. This study compared three wild type strains and one deficient in pneumolysin to explore the pathways of epithelial activation following a three hour infection in vitro.
2019-05-01 | E-MTAB-7841 | biostudies-arrayexpress
Project description:Describing the LACTB tumor suppressor activity in ovarian cancer cells
2022-10-02 | E-MTAB-12053 | biostudies-arrayexpress
Project description:In this study the root transcriptome profiles of young seedlings (5 days after germination at 23C) of two tomato species differing in cold tolerance were analysed and compared after a subsequent treatment for 3 days at 23 or 15C by RNAseq. Aim was to elucidate molecular mechanisms underlying root development associated with suboptimal-temperature tolerance during early seedling establishment.
2016-07-24 | E-MTAB-4855 | biostudies-arrayexpress
Project description:To gain insight into the gene signatures directly mediated by LAP (CEBPB) for cancer cell progression, we performed RNA-seq in LAP-HepG2 versus control cells.
2026-06-14 | E-MTAB-16207 | biostudies-arrayexpress
Project description:Background: Stem cells were often used for intervertebral disc degeneration (IDD) regeneration. The underlying mechanisms remain to be explored. LncRNAs were found to be related to the physiological process such as apoptosis and differentiation. Many studies focus on the messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) between normal nucleus pulposus and degeneration nucleus pulposus. However, few studies have shed light on the different expression of lncRNA and mRNA in the differentiation. In the present study, we aimed to determine mRNAs and lncRNAs, which are differentially expressed during in human adipose-derived mesenchymal stem cells (hADSCs) differentiation process into np-like cell types and to explore the related signaling pathways and the regulatory networks. Methods: hADSCs were induced to differentiation into np-like cell under the cytokine circumstance. The mark genes of np-like cell were determined by PCR and immunology staining. Then RNA-seq was used to analysis the expression of lncRNA and mRNA in the differentiation of hADSCs into np-like cell types. The significant genes were confirmed by Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Results: We found 14 lncRNAs and 601 mRNAs were significantly differentially expressed in hADSCs differentiation. The RNA-seq data were confirmed by real-time PCR. Furthermore, we found Gene Ontology terms were upregulated, and downregulated and significantly enriched pathways. Moreover, gene network shows significant differentially expressed genes. Meanwhile, the relationship of significantly changed mRNAs and lncRNAs were revealed by mRNA-lncRNA co-expression network. Conclusion: Our results first explore differentially expressed lncRNAs and mRNAs in the differentiation of hADSCs into np-like cell types. These may supply useful information for better understanding of stem cell therapy and IDD regeneration.
2025-08-18 | E-MTAB-15403 | biostudies-arrayexpress
Project description:In this study, we make used of mRNA-seq and its ability to reliably quantify isoforms, integrating this data with ribosome profiling and LC-MS/MS, to assign ribosome footprints and peptides at the isoform level. We leverage the principle that most cell types, and even tissues, predominantly express a single principal isoform to set isoform-level mRNA-seq quantifications as priors to guide and improve allocation of footprints or peptides to isoforms. Through tightly integrated mRNAseq, ribosome footprinting and/or LC-MS/MS proteomics we demonstrate that a principal isoform can be identified in over 80% of gene products in homogenous HEK293 cell culture and over 70% of proteins detected in complex human brain tissue. Defining isoforms in experiments with matched RNA-seq and translatomic/proteomic data increases the functional relevance of such datasets and will further broaden our understanding of multi-level control of gene expression. In this PRIDE submission you will find the raw files for the HEK293 cell proteomics. Files for the human brain proteomics can be found at PXD005445. We have also uploaded a zip file that contains the input files for our HEK293 cell analysis, and the isoform level output files – there is a separate folder within the zip files for these. The data used to create the manuscript figures is in the Rdata file. Code for assigning peptides and footprints to isoforms can be found on Github here: https://github.com/rkitchen/EMpire
2018-08-21 | PXD008693 | Pride
Project description:Role of sulfide under non photorespiratory conditions in Arabidopsis plants. Plants were grown under non photorespiratory conditions and transfered to active photorespiration conditions and were treated or not exogenously with NaHS.
2026-06-30 | E-MTAB-15916 | biostudies-arrayexpress