Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Noncoding RNA transcriptome analysis during cellular reprogramming

ABSTRACT: We report the application of single-cell and bulk RNA sequencing technology to examine the noncoding transcriptome of cells undergoing reprogramming to the pluripotent state. Examination of noncoding RNAs in reprogrammming cells. We examined iPS cells grown in standard ES cell culture conditions, as well as iPS cells grown in "2i" conditions (small molecule inhibition of Mek and Gsk3). We also compared our iPS samples to male and female ES cells (mES, fES).

ORGANISM(S): Mus musculus

SUBMITTER: Diane Trout

PROVIDER: E-GEOD-55291 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.

Kim Daniel H DH Marinov Georgi K GK Pepke Shirley S Singer Zakary S ZS He Peng P Williams Brian B Schroth Gary P GP Elowitz Michael B MB Wold Barbara J BJ

Cell stem cell 20150101 1

Cellular reprogramming highlights the epigenetic plasticity of the somatic cell state. Long noncoding RNAs (lncRNAs) have emerging roles in epigenetic regulation, but their potential functions in reprogramming cell fate have been largely unexplored. We used single-cell RNA sequencing to characterize the expression patterns of over 16,000 genes, including 437 lncRNAs, during defined stages of reprogramming to pluripotency. Self-organizing maps (SOMs) were used as an intuitive way to structure and ...[more]

PMID: 25575081

Similar Datasets

RNA-seq of Malassezia sympodialis

Project description:This data set is part of a study where the genome of Malassezia sympodialis (strain ATCC 42132) was sequenced using long-read technology and annotated using RNA-seq and proteogenomics. RNA was extracted at two different culture times (2 and 4 days). Seven RNA-seq libraries were prepared from independent samples. Two samples (P2 and P3) were enriched for protein-coding RNA using poly(A)-selection. The remaining five samples were processed with RiboMinus to deplete ribosomal RNA, and thus retain both mRNA and non-ribosomal noncoding RNA for sequencing. In total, we obtained 71 million RNA-seq read pairs mapping to genomic regions other than the highly expressed ribosomal loci.

2017-01-10 | E-MTAB-4589 | biostudies-arrayexpress

Rapid transcriptional response to physiological neuronal activity in vivo revealed by transcriptome sequencing

Project description:mRNA-seq of olfactory bulbs from odor-deprived and odor-stimulated mice (RNA-seq done in triplicates) Control mice were kept in a clean air environment (using an activated carbon filter). Stimulated mice were exposed to a cocktail of odorants for 30 minutes ("30 min" time point), or for 30 minutes followed by a period of 90 minutes of clean air ("120 min" time point.) Mice were sacrificed immediately at end of time point, and olfactory bulbs were dissected out for RNA extraction and RNA-FISH. Three adult mice (6-8 weeks of age or older) were used in each condition.

2014-06-27 | E-GEOD-58843 | biostudies-arrayexpress

Netrin-1 facilitates somatic cell reprogramming by limiting Dcc pro-apoptotic activity.

Project description:The generation of induced pluripotent stem (iPS) cells holds great promise in regenerative medicine. However, the relative flaws in the understanding of the molecular mechanisms promoting or limiting reprogramming still hinder the efficient generation of high quality iPS cells. Whereas modulation of the initial Oct4, Sox2, Klf4 and c-Myc (OSKM) cocktail with new transcription factors has been extensively documented, comparatively little is known about soluble molecules promoting the process, even if such recombinant factors could be highly valuable for therapeutic applications. In this study we developed a large-scale identification method to uncover novel programmed cell death (PCD)-related mechanisms limiting somatic cell reprogramming to pluripotency (SCRP). We identified Netrin-1 and its dependence receptor Dcc (Deleted in Colorectal Carcinoma), previously described for their respective survival/death functions both in normal and oncogenic contexts, as novel key SCRP modulators. We show that the early phase of SCRP is accompanied with a strong Netrin-1 deficiency, due to the improper epigenetic regulation of the Ntn1 promoter by OSKM. Mechanistically, we demonstrate that such Netrin-1 imbalance induces apoptosis mediated by the dependence receptor Dcc in a p53-independent manner. Correction of the Netrin-1/Dcc equilibrium by gain-of-ligand and loss-of-receptor experiments constrains apoptosis and improves reprogramming. As a consequence, we propose a novel iPS derivation protocol including a sequential treatment with recombinant Netrin1 that greatly facilitates the generation of mouse and human iPS cells. RNA-sequencing of mouse embryonic fibroblasts (passage 2 and passage 4), mouse pre-iPS cells (passage 5 and passage 25), 1 clone of control iPS (passage 5 and passage 25) and 2 independent clones of "Netrin-1 derived" iPS cells (passage 5 and passage 25). For this analysis, mouse iPS cell lines were grown in KSR+LIF media.

2015-09-01 | E-GEOD-54107 | biostudies-arrayexpress

Determination of the Lef1 regulated tanscriptome in differentiating ES cells

Project description:Lef1 is a critical transducer of the Wnt/beta-catenin signaling pathway that is essential for mesoderm differentiation in vertebrate embryos. We established a doxycycline inducible ES cell line to over-express Flag-tagged Lef1 in differentiating ES cells which have the capacity to form mesoderm cells in vitro. The goal of this study was to identify the genes/gene networks regulated by Lef1 to understand how it regulates mesoderm differentiation and to establish the Lef1-regulated, Wnt/beta-catenin transcriptome. Total RNA was extracted from ES cells after 3 days of differentiating following Lef1 over-expression from day 2 to 3. We compared the transcriptome of differentially expressed genes in untreated and doxycycline treated ES cells to identify Lef1 regulated genes.

2016-04-01 | E-GEOD-73083 | biostudies-arrayexpress

Determination of the Sp5 regulated transcriptome in differentiating ES cells

Project description:Sp5 is a target and critical transducer of the Wnt/beta-catenin signaling pathway and is essential for mesoderm differentiation in vertebrate embryos. We established a doxycycline inducible ES cell line to over-express Flag epitope-tagged Sp5 protein in differentiating ES cells which have the capacity to form mesoderm cells in vitro. The goal of this study was to identify the genes/gene networks regulated by Sp5 to understand how it regulates mesoderm differentiation by identifying important target genes which may mediate its activity. Total RNA was extracted from ES cells after 3 days of differentiating following F-Sp5 over-expression from day 2 to 3. We compared the transcriptome of differentially expressed genes between untreated (minus) and doxycycline treated (plus) ES cells to identify Sp5 regulated genes.

2016-04-01 | E-GEOD-73082 | biostudies-arrayexpress

Systematic RNA-seq analysis of the early events of CD4+ T cell activation

Project description:RNA-seq was used to look at the transcriptome changes and the early events of T cell receptor stimulation in CD4+ T cells CD4+ T cells were stimulated with immobilised anti-CD3/CD28 antibodies for 4 hours and RNA was extracted and subjected to RNA-seq analysis.

2012-08-08 | E-GEOD-34550 | biostudies-arrayexpress

RNA profiling for mouse B10+ cells and B10- B cells

Project description:we used genome-wide transcriptome analysis to profile the mRNA, long noncoding RNA (lncRNA), and microRNA (miRNA) expression of B10 cells, an antigen-specific Cd1dhiCd5+Cd19hiIl10 competent regulatory B cell. Potential key upstream regulators (including transcription factors, cytokines, trans-membrane receptors, and kinases) for Breg biogenesis and function were identified. B10+ B cells (Cd1dhiCd5+Cd19hiIl10+) and B10- cells (Cd1d-Cd5-Cd19hiIl10-) from mouse splenic B cell were sorted for RNA preparation. Two independent repeats were prepared for RNA-seq

2015-10-29 | E-GEOD-63426 | biostudies-arrayexpress

RAG Represents a Widespread Threat to the Lymphocyte Genome - (RNA-seq)

Project description:The RAG1 endonuclease, together with its cofactor RAG2, is essential for V(D)J recombination but is a potent threat to genome stability. The sources of RAG1 mistargeting and the mechanisms that have evolved to suppress it are poorly understood. Here, we report the surprising finding that RAG1 binds to thousands of sites in the genome of developing lymphocytes, primarily at active promoters and enhancers. The genome has responded by reducing the abundance of "cryptic" recombination signals near sites of RAG1 binding. This depletion operates specifically on the RSS heptamer, with nonamers enriched at RAG1 binding sites. Reversing this RAG-driven depletion of cleavage sites by insertion of strong recombination signals creates an ectopic hub of RAG-mediated V(D)J recombination and chromosomal translocations. Our findings delineate rules governing RAG binding in the genome, identify areas at risk of RAG-mediated damage, and highlight the evolutionary struggle to accommodate programmed DNA damage in developing lymphocytes. RNA-seq profiles of mouse thymocytes

2015-08-06 | E-GEOD-69473 | biostudies-arrayexpress

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [RNA-seq]

Project description:Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. Therefore, it becomes indispensable to exploit other reliable molecular markers for evaluating the quality of iPS cells accurately. In the present study, we successfully utilize the sequential reprogramming approach and produce all-iPS mice to six generations using iPS cell lines derived from different cell lineages which contain the same proviral integration in the genome. By comparing the global gene expression and epigenetic modifications of both "tetra-on" and corresponding "tetra-off" iPS cell lines established from either mesenchymal or hematopoietic lineages through deep sequencing analysis of mRNA expression, small RNA profiling, histone modifications (H3K4m2, H3K4me3 and H3K27me3) and DNA methylation, very few differences are detected among all the iPS cell lines investigated. However, we find that two imprinted genes, disruption of which correlate with the reduced pluripotency of iPS cells. Therefore, our data not only provide the first demonstration that producing of all-iPS mice to six generations is feasible, but reveal that two imprinted regions can be served as pluripotency markers of iPS cells. Examination of the mRNA expression in 13 cell types

2013-12-06 | E-GEOD-36290 | biostudies-arrayexpress

Transcriptome changes in IL-10 treated peritoneal macrophages

Project description:To try to identify the mechanism of STAT3s indirect action we have used a genomic approach to map the binding sites of STAT3 within the genome and also used RNA-seq technology to map the changes in RNA expression and transcript isoform abundance in response to IL-10. Examination of transcriptome changes in peritoneal macrophages when treated with IL-10 for 4 hours. RNA was extracted and sequenced.

2012-02-13 | E-GEOD-31530 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data