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LncRNA profile study during Human MSC adipogenic differentiation: Day0 vs Day3 vs Day6

ABSTRACT: LncRNA transcriptional profiling of human mesenchymal stem cells comparing control undifferentiated HMSC with Day3 and Day6 adipogenic differentiation stages Three-condition experiment, Day0 vs. Day3 vs Day6 cells. Day0: 4 replicates, Day3: 3 replicates and Day6: 3 replicates.

ORGANISM(S): Homo sapiens

SUBMITTER: Runsheng Chen

PROVIDER: E-GEOD-57593 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Homo sapiens

Project description:LncRNA profile study during Human MSC adipogenic differentiation: Day0 vs Day3 vs Day6

| PRJNA246745 | ENA

LncRNA profile study during Human MSC adipogenic differentiation: Day0 vs Day3 vs Day6

Project description:LncRNA transcriptional profiling of human mesenchymal stem cells comparing control undifferentiated HMSC with Day3 and Day6 adipogenic differentiation stages

2014-05-22 | GSE57593 | GEO

RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis- and Adipose-derived Stromal Stem Cells

Project description:Background: Tissue regeneration and recovery in the adult body depends on self-renewal and differentiation of stem and progenitor cells. Mesenchymal stem cells (MSCs) that have the ability to differentiate into various cell types, have been isolated from the stromal fraction of virtually all tissues. However, little is known about the true identity of MSCs. MSC populations exhibit great tissue-, location- and patient-specific variation in gene expression and are heterogeneous in cell composition. Methodology/Principal findings: Our aim was to analyze the dynamics of differentiation of two closely related stromal cell types, adipose tissue-derived MSCs and dermal fibroblasts (FBs) along adipogenic, osteogenic and chondrogenic lineages using multiplex RNA-seq technology. We found that undifferentiated donor-matched MSCs and FBs are distinct populations that stay different upon differentiation into adipocytes, osteoblasts and chondrocytes. The changes in lineage-specific gene expression occur early in differentiation and persist over time in both MSCs and FBs. Further, MSCs and FBs exhibit similar dynamics of adipogenic and osteogenic differentiation but different dynamics of chondrogenic differentiation. Conclusion: Our findings suggest that stromal stem cells including adipose-derived MSCs and dermal FBs exploit different molecular mechanisms of differentiation to reach a common cell fate. The early mechanisms of differentiation are lineage-specific and are similar for adipogenic and osteogenic differentiation but are distinct for chondrogenic differentiation between MSCs and FBs. A total of 91 samples were analyzed by multiplex RNA-seq. Samples represented replicates from two patients, two cell types and three differentiation protocols, as indicated by the sample annotation. 5 barcodes were unused, but the corresponding FASTQ files are included for completeness.

2012-06-27 | E-GEOD-37521 | biostudies-arrayexpress

A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules

Project description:Adipose stem cells (ASCs) and adipocytes play a crucial role in maintaining energy balance. We aim to examine the temporal relationship between gene expression and histone modification transitions during in vitro differentiation of human ASCs into adipocytes. Here, we examine by RNAseq proliferating ASCs (Day -2 prior to adipogenic induction), confluent ASCs (Day 0, adipogenic induction), pre-adipocytes (Day 3) and maturing adipocytes (Day 9). We find 1060, 5452 and 2216 genes differentially expressed between D-2/D0, D0/D3 and D3/D9 respectively. We identify gene clusters with distinct and dynamic expression patterns. In particular, adipogenic induction is marked by temporal waves of gene induction and downregulation. We report two types of transcriptional waves: (i) those showing transient induction or inactivation at D0, D3 or D9, and involved in sensory perception and immune response functions; and (ii) those showing long-lived induction or repression at these time points. Our data reveal a dynamic network of gene regulation during adipogenesis, involving signaling, immune and developmental processes. We identify 15 unique epigenetic states using Hidden Markov Modeling which reflects an epigenetically highly organised genome showing enhancer states are commonly consecutive. A heatmap for the abundance of epigenetic states for the expression clusters reveals a link between expression and epigenetic marking of the state suggesting an increase in the number of number of chromatin states with increase in expression. Our data point to a model of increased epigenetic complexity associated with gene expression. Examination of expression of profiles of ASCs across differentiation

2014-12-10 | E-GEOD-60237 | biostudies-arrayexpress

Murine uterus expression profile during Peri-implantation: Pre-implantation vs. Post-implantation

Project description:Anaylsis differentially expressed genes of mouse peri-implanted uteri comparing pre-implantation uteri (Day2, Day3 and Day4) with post-implantation uteri (Day6, Day7 and Day8) by microassay. This study has built a meaningful basis for future investigation in elucidating the molecular nature of maternal-fetal interactions during pregnancy establishment and maintenance. Pre-implantation uteri VS. Post-implantation uteri. Three biological replicates of each experiments: pre-implantation uteri (Day2, Day3 and Day4): 234, 234①, 234②; 3 mixture of post-implantation uteri (Day6, Day7 and Day8): 678, 678①, 678②. Two hybridizations were performed by using a reverse fluorescence strategy (Cy3, Cy5) for each sample.

2011-06-30 | E-GEOD-26615 | biostudies-arrayexpress

Comparison of HEK293T cells grown in serum supplemented media to cells serum starved for 3 days

Project description:HEK293T cells grown to confluence in media +10% fetal bovine serume. Media was removed and replaced with serum free media, and cultured for 3 days. RNA was harvested from day0 (serum supplemented), control, and day3 (serum starved) cultures, experiment.

2014-12-13 | GSE64117 | GEO

Murine uterus expression profile during Peri-implantation: Pre-implantation vs. Post-implantation

2011-06-30 | GSE26615 | GEO

Gene epression profile of s-spheroids and t-spheroids differentiated from iPS cells

Project description:For definitive endoderm differentiation, iPS cells (day0) were treated with 100 ng ml-1 activin A and 3μM CHIR99021 for 1 day and 100 ng ml-1 activin A for the following two days. Definitive endoderm was subsequently treated with 3uM CHIR99021 and 500ng ml-1 FGF4 for mid/hindgut differentiation. Mid/hindgut floating spheroids (fl; t-Spheroids) were collected from culture medium from day6 to day 8. On day6, mid/hindgut cells were dissociated into single cells and seeded onto EZSPHERE plate to generate suspension spheroids(EZ; s-Spheroids). RNA of fl spheroids and EZ spheroids were extracted using QIAGEN RNeasy kit.

2022-11-15 | GSE182230 | GEO

Transcription profiling time series of human epithelial cells during development

Project description:The experiment was designed to generate a time series for epithelial model during development. Each time point had 3 replicates. The data set contained 5 time points over 10 days. They are day0, day3, day5,day7,day10.

2009-01-01 | E-MEXP-1130 | biostudies-arrayexpress

Quantification of basal RNA mutation rate in the repRNA-v4 EGFP region

Project description:REPLACE was engineered from an orthogonal alphaviral RNA replication system. It generates a large, continuously diversified library of replicative RNAs through a replicase-limited mode of replication and inducible mutagenesis. We analyzed the mutation frequency at Day0 (IVT RNA), Day1, Day3, Day7, Day14, Day21 and DNA plasmid to estimate the RNA mutation rate. This data was used to guide the construction of RNA mutant libraries.

2024-09-30 | GSE271880 | GEO

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