Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Examining serotonergic neuron differentiation from human iPSCs

ABSTRACT: The goals of this study were to study serotonergic neuron differentiation from patient derived iPSCs

OTHER RELATED OMICS DATASETS IN: PXD008106

ORGANISM(S): Homo sapiens

PROVIDER: GSE117910 | GEO | 2019/01/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Examining serotonergic neuron differentiation from human iPSCs

Project description:Examining serotonergic neuron differentiation from human iPSCs

| PRJNA483556 | ENA

The divergent nodes of non-autonomous UPRER signaling through serotonergic and dopaminergic neurons

Project description:Performed RNA-seq analysis of animals with xbp-1s overexpression (ER stress response transcription factor) in specific neuron types: pan-neuronal, serotonergic neuron, dopaminergic neuron, and both serotonergic and dopaminergic neurons, all compared to a wild-type control. RNA-seq was performed on purified RNA extracted from ~1000 whole worms using a proprietary Genewiz protocol described briefly in the manuscript. 3 biological replicates are provided for each sample.

2021-01-01 | E-MTAB-9771 | biostudies-arrayexpress

Altered serotonergic circuitry in SSRI-resistant major depressive disorder patient-derived neurons

Project description:The goals of this study are to generate and study serotonergic neurons from MDD patients that are selective serotonin reuptake inhibitor (SSRI) remitters and SSRI-nonremitters (NR).

2022-02-12 | GSE126512 | GEO

Sequential expression profile of cortical neuron differentiation from human induced pluripotent stem cells (iPSCs) by RNA-Seq

Project description:We aim to profile the dynamic changes of gene expression dynamics during cortical neuron differentiation from human iPSCs. We used RNA-seq to map open chromatins in iPSCs, neural stem cells (NSCs) at day 33 and day 41.

2018-04-24 | GSE102352 | GEO

Mapping open chromatin dynamics of cortical neuron differentiation from human induced pluripotent stem cells (iPSCs) by ATAC-Seq

Project description:We aim to profile the dynamic changes of chromatin accessibility (openness) to transcription factors during cortical neuron differentiation from human iPSCs. We used ATAC-seq to map open chromatins in iPSCs, neural stem cells (NSCs) at day 27 and day 33 of neural induction (designated as iN-d30 for simplicity), and neurons at day 41 (iN-d41). We found that there were robust dynamic changes of open chromatins that are corresponding to cell stage-specific gene function both at genome-wide level and at individual loci of interest to neurodevelopment and psychiatric disorders, with NSC (iN-d30) gaining most (89%) of the neuron specific open chromatin peaks. Open chromatin peaks shared by different cell stages were overrepresented in core promoters, while the peaks specific to each cell stage or showing dynamic change of openness were enriched in introns and intergenic sequences. The dynamic change of open chromatins is orchestrated by specific sets of transcription factors (TFs) in each cell stage, providing epigenomic support the central role of NEUROD1 and NEUROG2 in cortical neuron differentiation.

2017-07-27 | GSE70823 | GEO

Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments after spinal cord injury

Project description:The goals of this study is to compare transcriptome profiles (RNA-seq) of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments after spinal cord injury. Bulk RNA-Seq samples of ISNs from the injury area and residual segments respectively were FAC-sorted from Tg(tph2:GFP) line. Total RNA was isolated using SMART-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech). Sequencing libraries (N=5-6) were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB). We mapped about 50-60 million sequence reads per sample to the zebrafish genome and identified 39,714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments after spinal cord injury.

2021-11-08 | GSE182869 | GEO

Expression data of Glutarmatergic neuron and GABAergic neruon induced from iPSCs

Project description:Expression data of Glutarmatergic neuron and GABAergic neruon induced from iPSCs

| PRJNA480293 | ENA

Multiplex single cell analysis of serotonergic neuron function in planarians reveals widespread effects in diverse cell types

Project description:We used scRNA-seq to examine serotonergic function in asexual planarians. We profiled 47,292 single cell transcriptomes of planarian of 3 different RNAi categories: gfp(RNAi), lhx1/5-1(RNAi) and pitx(RNAi). We detected changes in cell type frequency and gene expression patterns in planarian of different knock-down conditions, capturing regulatory programs of distinct cell types in response to loss of serotonergic function.

2024-02-19 | GSE256032 | GEO

Establishment of a dopaminergic neuron purification system in mice

Project description:Transcriptomic analysis of enriched of neuron population collected from in-vivo mouse brains has been a challenge in the neuroscience field due to its fragility in withstanding harsh condition during isolation and collection process. We established a fluorescent reporter mouse Ddc-hKO1 to facilitate the identification and collection of Ddc-expressing neurons (dopaminergic, serotonergic, cholinergic and adrenergic neurons) by the detection of red fluorescence signals using a FACs. We utilized an improved isolation protocol that ensure high yield and quality of viable neurons during collection that is suitable for RNA-sequencing. This is the first report of transcriptomic profiling of Ddc expressing (hKO1(+)) neurons. Successful collection of Ddc-expressing neurons were verified by gene markers of dopaminergic, serotonergic, cholinergic neurons in hKO1(+) populations while other neuron types in hKO1(-) population. Furthermore, GSEA analysis were performed on both hKO1(+) and hKO1(-) to further support the neuron types collected in respective population.

2022-11-28 | GSE171581 | GEO

Transcriptional profiling of human serotonergic neurons in vitro

Project description:Human serotonergic neurons are derived using published transdifferentiation protocols. Human Fibroblasts correspond to human fibroblasts (from Line#1, Coriell bought (AG08498)). Samples labeled human neurons or induced neurons (iN) correspond to neurons transdifferentiated from fibroblasts using two transcription factors, as previously described (#1-AG08498 or #2:ERF-1, Erlangen Germany, a line given to us by collaborators) into primarily glutamatergic neruons. Samples labled 5-HT neurons or serotonergic neurons or iSN correspond to serotonergic neurons derived from the stated fibroblast lines, using an additional four transcription factors. For transdifferentiation of iN and iSN, fibroblasts were made to overexpress the stated transcription factors in a doxycycline inducible manner for up to 3 weeks, and then neurons are sorted out and collected directly into Trizol for RNA preparation and sequencing. The non-transdifferentiated fibroblast lines were collected in bulk withtout differentiation into neurons. The line number corresponds to the same fibroblast line either being transdifferentiated into iN or iSN, as labeled - for direct and groupwise comparison.

2016-02-02 | E-MTAB-3680 | 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