RNA-seq data from healthy and DMD human cells, along skeletal muscle differentiation from induced pluripotent stem cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Homo sapiens
SUBMITTER: Virginie Mournetas
PROVIDER: E-MTAB-8321 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:3 or 4 healthy cells - 3 DMD cells - 7 time points (tissue-derived myoblasts, tissue-derived myotubes, hiPSCs, Day 3 of differentiation, Day 10 of differentiation, Day 17 of differentiation, Day 25 of differentiation).
2020-10-05 | E-MTAB-8293 | biostudies-arrayexpress
Project description:HiPSCs and human myoblast cells were differentiated into myocytes, and the global gene expression profile were analyzed. Comparison of gene expressions among 8 experiments, 3 were derived from hiPSCs(cell line; 253G1), 1 was derived from hiPSCs(cell line; 253G4), 1 was derived from hiPSCs(cell line; 201B7), 2 were from human myoblast cell line (Hu5/E18) and 1 was undifferentiated hiPSCs.
2013-04-01 | E-GEOD-43183 | biostudies-arrayexpress
Project description:Immunodeficiency, Centromeric Instability, and Facial Anomalies Type I (ICF1) Syndrome is a rare genetic disease caused by mutations in DNMT3B, a de novo DNA methyltransferase. However, the molecular basis of how DNMT3B-deficiency leads to ICF1 pathogenesis is unclear. Induced pluripotent stem cell (iPSC) technology facilitates the study of early human developmental diseases via facile in vitro paradigms. Here, we generate iPSCs from ICF Type 1 Syndrome patient fibroblasts followed by directed differentiation of ICF1-iPSCs to mesenchymal stem cells (MSCs). By performing genome-scale bisulfite sequencing, we find that DNMT3B-deficient iPSCs exhibit global loss of non-CG methylation and select CG hypomethylation at gene promoters and enhancers. Further unbiased scanning of ICF1 iPSC methylomes also identifies large megabase regions of CG hypomethylation typically localized in centromeric and subtelomeric regions. RNA sequencing of ICF1 and control iPSCs reveals abnormal gene expression in ICF1 iPSCs relevant to ICF Syndrome phenotypes, some directly associated with promoter or enhancer hypomethylation. Upon differentiation of ICF1 iPSCs to mesenchymal stem cells (MSCs), we find virtually all CG hypomethylated regions remained hypomethylated when compared to either wild-type iPSC-derived MSCs or primary bone-marrow MSCs. Collectively, our results show specific methylome and transcriptome defects in both ICF1-iPSCs and differentiated somatic cell lineages, providing a valuable stem cell system for further in vitro study of the molecular pathogenesis of ICF1 Syndrome. MethylC-seq and RNA-Seq in ICF Syndrome patient fibroblast derived induced pluripotent stem cells.
2014-11-17 | E-GEOD-46030 | biostudies-arrayexpress
Project description:Adipose tissue plays a critical role in growth, energy metabolism, and carcass composition in pigs. However, the age-dependent molecular mechanisms underlying backfat development remain poorly characterized, particularly in native breeds such as the Ningxiang pig, which exhibits high fat deposition and distinct growth patterns. This study aimed to characterize the dynamic proteomic changes in backfat tissue across postnatal development and identify molecular pathways and candidate proteins associated with economically important carcass traits. We performed a comprehensive proteomic analysis of backfat tissue collected from Ningxiang pigs across seven postnatal developmental stages (day 60 to 360). Using high-resolution mass spectrometry, we quantified dynamic changes in protein abundance and explored their functional relevance through gene ontology (GO) enrichment and network-based analyses. Principal component analysis revealed clear age-related separation in proteomic profiles, particularly between early (day 60–120) and later developmental stages. GO enrichment analysis of differentially abundant proteins indicated significant overrepresentation of biological processes related to energy metabolism, translation, immune response, and mitochondrial function in older age groups. Further curation of lipid metabolism pathways identified hundreds of proteins involved in lipogenesis and lipolysis, many of which displayed distinct age-dependent expression patterns. To link protein expression to economically important traits, we performed weighted gene co-expression network analysis (WGCNA), identifying four protein modules significantly associated with carcass characteristics such as lean meat percentage, fat content, and carcass weight. From these modules, we identified four key hub proteins— ALDH18A1, FABP4, FBP1, and HADHB—with known roles in lipid transport, gluconeogenesis, amino acid metabolism, and fatty acid oxidation, respectively. This study provides novel insights into the proteomic remodeling of backfat during postnatal development and highlights potential molecular targets for improving carcass quality in pigs. Our findings contribute to a deeper understanding of adipose tissue biology and offer a valuable resource for future genetic and breeding strategies.This study provides the first in-depth proteomic characterization of backfat development across seven postnatal stages in Ningxiang pigs, a native Chinese breed known for high fat deposition. By integrating high-resolution mass spectrometry with gene ontology and co-expression network analyses, we uncovered dynamic, age-dependent changes in protein abundance linked to key biological processes, including energy metabolism, immune function, and mitochondrial activity. Notably, we identified four protein modules significantly associated with carcass traits such as lean meat percentage and fat content, and highlighted four hub proteins (ALDH18A1, FABP4, FBP1, and HADHB) as potential molecular markers for selective breeding. These findings advance our understanding of adipose tissue biology and provide actionable molecular targets for improving carcass composition in pigs. The work also offers a valuable reference dataset for future functional genomics and precision breeding efforts in indigenous and commercial pig populations.
2026-06-08 | PXD067020 | Pride
Project description:Cell differentiation is based on a synchronised orchestra of complex pathways of intrinsic and extrinsic signals that manifest in the induced expression of specific transcription factors and pivotal genes within the nucleus. One cannot ignore the epigenetic status of differentiating cells, comprising not only histones and DNA modifications but also the spatial and temporal intranuclear chromatin organisation, which is an important regulator of nuclear processes. In the present study, we investigated the nuclear architecture of human primary myoblasts and myocytes in an in vitro culture, with reference to global changes in genomic expression. Repositioning of the chromosomal centromeres, along with alterations in the nuclear shape and volume, was observed as a consequence of myotube formation. Moreover, the microarray data showed that during in vitro myogenesis cells tend to silence rather than induce gene expression. The creation of a chromosome map marked with gene expression changes that were at least 2-fold confirmed the observation. Additionally, almost all of the chromosomal centromeres in the differentiated cells preferentially localised near the nuclear periphery when compared to the undifferentiated cells. The exceptions were chromosomes 7 and 11, in which we were unable to confirm the centromere repositioning. In our opinion, this is the first reported observation of the movement of chromosomal centromeres along differentiating myogenic cells. Based on these data we can conclude that the myogenic differentiation with global gene expression changes is accompanied by the spatial repositioning of chromosomes and chromatin remodelling, which are important processes that regulate cell differentiation. Six samples from human skeletal muscle stem cells populations before and after differentiation were analysed
2013-04-06 | E-GEOD-45819 | biostudies-arrayexpress
Project description:Olive (Olea europaea L.) is one of the most economically relevant tree crops in the Mediterranean basin. In this study, a comparative proteomic along with metabolomic-wide investigation was carried out on drupes of Greek olive cultivar 'Chondrolia Chalkidikis', collected across six developmental stages (S), namely seed development (S1, S2), mesocarp development (S3, S4, S5) and full maturation (S6). These stages were first characterized through the dynamics of fruit weight, dimensions and color parameters such as lightness, redness and yellowness. Combined gas chromatography–mass spectrometry and reversed–phase liquid chromatography quadrupole–time–of–flight mass spectrometry (RPLC–QToF–MS) procedures quantified 47 primary (e.g. allose, galactose, quinic acid, sorbitol, stearic acid) and 21 secondary (e.g. elenolic acid, oleacin, rutin, luteolin, hydroxytyrosol) metabolites in mesocarp samples during development. Protein analysis via nano–LC coupled to HDAM Orbitrap mass spectrometer, identified 3258 proteins from which the 350 were differentially accumulated between the final maturation stages (S5 and S6). Olive genome-based functional annotation showed that the largest proportion of identified proteins were involved in primary metabolism [i.e. lipoxygenases (LOX1/5)], energy [i.e. ferredoxin NADP+ reductase (FNR)], signal transduction [i.e. serine/threonine kinases (SAPK2, SRK2A, STK), transcription [i.e. elongation factor 2 (EEF2)] and protein destination [i.e. serine carboxypeptidase (SCPL)]. This investigation provides a reference framework for further nutritional and breeding studies, also allowing cross comparison among other olive cultivars.
2021-11-25 | PXD021086 | Pride
Project description:Transcript abundance profiling analysis of bovine early embryonic development in vivo using a bovine developmental array.
2009-06-01 | E-MEXP-2075 | biostudies-arrayexpress
Project description:The metabolite beta-aminoisobutyric acid (BAIBA) as an exercise-induced muscle-derived signal regulating adipose tissue metabolism during exercise. Here, we determine that BAIBA mimics aerobic exercise training effects on human skeletal myocytes.
2026-06-22 | E-MTAB-14746 | biostudies-arrayexpress
Project description:An alternative promoter of the PGC-1 alpha gene gives arrise to 3 new isofroms of the PGC-1 alpha gene refered to as PGC-1a2 (A2), PGC-1a3 (A3) and PGC-1a4 (A4). The proximal PGC-1 alpha promotor transcribes the canonical PGC-1 alpha which is refered to as PGC-1a1 (A1).G1/G2/G3 samples refer to the Green fluorescent protein (GFP) control samples used in this experiment. Forced expression of specifically PGC-1a4 isoform results in muslce hypertrophy associated with increased IGF-1 signaling and repression of myostatin signaling. Adnoviral over expression assays were performed on primary myoblasts from C57BL/6 mice for each of the PGC-1 alpha isoforms originating from the proximal or alternative promotor.
2012-12-04 | E-GEOD-42473 | biostudies-arrayexpress
Project description:Investigate differences in chromatin accessibility during development in E16 and L3 neurons
2023-12-01 | E-MTAB-13491 | biostudies-arrayexpress