Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Timeline RNAseq of fibroblast to neuron direction conversion

ABSTRACT: Timeline RNAseq to identify gene expression dynamics over the course of conversion of fibroblasts into induced neurons.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Joseph Herdy

PROVIDER: E-MTAB-7259 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Timeline RNAseq of fibroblast to neuron direction conversion

Project description:Timeline RNAseq of fibroblast to neuron direction conversion

| PRJEB32551 | ENA

RNA-seq timeline of fibroblast to neuron conversion using traditional NC media and NC+ZPAK media

Project description:Bulk RNA was extracted via trizol at Fibroblasts stage, 5 days, 10 days, 15 days, and 20 days of fibroblast to neuron conversion using traditional NC media, or NC media supplemented with ZM336372, pyrintegrin, AZ960, and KC7F2

2019-05-23 | E-MTAB-7250 | biostudies-arrayexpress

RNA-seq timeline of fibroblast to neuron conversion using traditional NC media and NC+ZPAK media

Project description:RNA-seq timeline of fibroblast to neuron conversion using traditional NC media and NC+ZPAK media

| PRJEB32695 | ENA

Mitochondrial reprogramming using dCas9 boosts glia-to-neuron conversion

Project description:Astrocyte-to-neuron conversion has developed into a promising avenue for neuronal replacement therapy. Neurons depend critically on mitochondria function and often die by ferroptosis during the conversion process. Here we examined the extent of adequate mitochondrial reprogramming by morphology and proteome analysis. While mitochondria profoundly changed their morphology during Neurogenin2 (Neurog2) – or Achaete-scute homolog 1 (Ascl1)-mediated astrocyte-to-neuron reprogramming, we found neuron-specific mitochondrial proteins, here identified in a comprehensive proteome analysis of isolated mitochondria from primary neurons and astrocytes, to be only partially and at late stages regulated during the process. To improve this, we used dCas9 technology to induce neuron-specific mitochondrial proteins early during reprogramming. This resulted not only in increased conversion efficiency, but also in faster neuronal generation. Taken together, reprogramming mitochondria in a cell type-specific manner has powerful effects on astrocyte-to-neuron conversion, suggesting mitochondria to be a driving force in this process.

2021-03-29 | PXD014886 | Pride

Attenuation of PTBP2 facilitates fibroblast to neuron conversion by promoting alternative splicing of neuronal genes

Project description:The direct conversion of human skin fibroblasts to neurons has a low efficiency and unclear mechanism. Here, we show that the knockdown of PTBP2 (nPTB) significantly enhanced the transdifferentiation induced by ASCL1, MiR124-9/9* and p53 shRNA to generate mostly GABAergic neurons. Longitudinal RNAseq analyses identified the continuous induction of many RNA Splicing Regulators (RSRs). Among these, the knockdown of RBFOX3, which encodes the mature neuronal marker NeuN, significantly abrogated the transdifferentiation. Overexpression of RBFOX3 significantly enhanced the conversion induced by AMp; the enhancement was occluded by PTBP2 knockdown. We found that PTBP2 attenuation significantly favored neuron-specific alternative splicing (AS) of many genes involved in synaptic transmission, signal transduction, and axon formation. RBFOX3 knockdown significantly reversed the effect, while RBFOX3 overexpression enhanced it. The study reveals the critical role of neuron-specific AS in the direct conversion of human skin fibroblasts to neurons by showing that PTBP2 attenuation enhances this mechanism in concert with RBFOX3.

2023-10-12 | GSE210131 | GEO

Dissecting engineered cell types and enhancing cell fate conversion via CellNet

Project description:Engineering clinically relevant cells in vitro holds promise for regenerative medicine, but most protocols fail to faithfully recapitulate target cell properties. To address this, we developed CellNet, a network biology platform that determines whether engineered cells are equivalent to their target tissues, diagnoses aberrant gene regulatory networks, and prioritizes candidate transcriptional regulators to enhance engineered conversions. Using CellNet, we improved B cell to macrophage conversion, transcriptionally and functionally, by knocking down predicted B cell regulators. Analyzing conversion of fibroblasts to induced hepatocytes (iHeps), CellNet revealed an unexpected intestinal program regulated by the master regulator Cdx2. We observed functional engraftment of mouse colon by iHeps, thereby establishing their broader potential as endoderm progenitors and demonstrating direct conversion of fibroblasts into intestinal epithelium. Our studies illustrate how CellNet can be employed to improve direct conversion and to uncover unappreciated properties of engineered cells. 15 samples

2014-08-14 | E-GEOD-59037 | biostudies-arrayexpress

Methylation array of young, mid age, and old induced neurons cultured in NC+ZPAK, as well as unconverted old and young fibroblast

Project description:Methylation array was used to quantify CpG methylation to determine if NC+ZPAK media was affecting the age of the donor after neuron conversion. Beta values were determined using the ChAMP methylation analysis pipeline.

2018-10-04 | E-MTAB-7226 | biostudies-arrayexpress

PTBP2 attenuation facilitates fibroblast to neuron conversion by promoting alternative splicing of neuronal genes.

Project description:The direct conversion of human skin fibroblasts to neurons has a low efficiency and unclear mechanism. Here, we show that the knockdown of PTBP2 significantly enhanced the transdifferentiation induced by ASCL1, MIR9/9∗-124, and p53 shRNA (AMp) to generate mostly GABAergic neurons. Longitudinal RNA sequencing analyses identified the continuous induction of many RNA splicing regulators. Among these, the knockdown of RBFOX3 (NeuN), significantly abrogated the transdifferentiation. Overexpression of RBFOX3 significantly enhanced the conversion induced by AMp; the enhancement was occluded by PTBP2 knockdown. We found that PTBP2 attenuation significantly favored neuron-specific alternative splicing (AS) of many genes involved in synaptic transmission, signal transduction, and axon formation. RBFOX3 knockdown significantly reversed the effect, while RBFOX3 overexpression occluded the enhancement. The study reveals the critical role of neuron-specific AS in the direct conversion of human skin fibroblasts to neurons by showing that PTBP2 attenuation enhances this mechanism in concert with RBFOX3.

| S-EPMC10679656 | biostudies-literature

Direct cell conversion from human dermal fibroblast to adipocyte

Project description:To investigate the effect of ZNF395 on adipogenesis, we tested whether ZNF395 enhance cell conversion from human dermal Fibroblast (FIB) to Adipocyte (ADP). PPARG2 was reported as a master regulator and can induce adipogenesis in non-adipogenic fibroblasts. We transduced PPARG2 with or without ZNF395 in FIB with lentivirus. Interestingly, co-transduction of PPARG2 and ZNF395 showed higher occurrence of adipocyte-like cells as compared with PPARG2 alone. Moreover, genes related with lipid metabolic process and lipid transport was significantly up-regulated in combination of PPARG2 and ZNF395. These results suggest that ZNF395 co-ordinate the transcriptional regulatory pathway with PPARG2, necessary for the induction of adipogenesis. Total RNA was obteined from human dermal fibroblast transduced with mock lentivirus vector (FIB_ctrl), PPARG2 (FIB_PPARG2) and co-transduced with PPARG2 and ZNF395 (FIB_PPARG2+ZNF395).

2012-12-01 | E-GEOD-37925 | biostudies-arrayexpress

Small molecules increase direct neural conversion of human fibroblasts

Project description:Time course micro array experiment to identify transcriptional changes in response to exposure of hFLs to different combinations of small molecules during direct neuronal reprogramming hFL1 cells were transduced with conversion factors Ascl1, Brn2a and Myt1L and five days after transduction, transgene expression was activated by doxycycline. On day 3 of transgene expression, MEF medium was replaced by N2B27 medium plus small molecules, depending on the condition. Ascl1 expression was linked to GFP so that all GFP pos cells were FACS isolated at different times of exposure to small molecules (or N2B27 medium in transgene only groups). Post FACS, cells were lysed and total RNA was extracted and used as input for micro array experiments.

2016-07-30 | E-GEOD-83896 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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