Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk RNA-seq NOHA

ABSTRACT: Bulk RNA sequencing (bulk RNA-seq) data of the Neural Organoid Hormonal Atlas (NOHA). To investigate the impact of hormonal modulation on neurodevelopmental processes, we used neural organoids derived from two genetically validated human induced pluripotent stem cell (hiPSC) control lines (CTL08, male; CTL04, female). Organoids were chronically exposed to agonists and inhibitors targeting seven hormone signaling pathways known to regulate human brain development: androgen, estrogen, glucocorticoid, thyroid, retinoic acid, liver X, and aryl hydrocarbon. Appropriate negative controls were included, consisting of vehicle-treated (DMSO) and untreated samples (CTL). GitHub: https://github.com/GiuseppeTestaLab/noha

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Gaja Matassa

PROVIDER: E-MTAB-17185 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNAseq NOHA

Project description:To investigate the impact of hormonal modulation on neurodevelopmental processes, we performed single-cell RNA sequencing (ScRNA-seq) on neural organoids derived from two genetically validated human induced pluripotent stem cell (hiPSC) control lines (CTL08, male; CTL04, female). Organoids were chronically exposed to agonists and inhibitors targeting seven hormone signaling pathways known to regulate human brain development: androgen (AND), estrogen (EST), glucocorticoid (GC), thyroid (THY), retinoic acid (RA), liver X (LX), and aryl hydrocarbon (AH). Appropriate negative controls were included, consisting of vehicle-treated (DMSO) and/or untreated samples depending on the experimental condition. GitHub: https://github.com/GiuseppeTestaLab/noha Cellxgene: https://cellxgene.cziscience.com/collections/2bebc4ae-69a2-4001-9d2f-091ec9b4020c

2026-07-22 | E-MTAB-17184 | biostudies-arrayexpress

Bulk ATAC-seq of primate cerebral organoids

Project description:Bulk ATAC-seq was performed on human, chimpanzee, bonobo, and macaque stem cell-derived cerebral organoids. ATAC-seq was performed on day 60 (2 months old) and day 120 (4 months old) cerebral organoids.

2019-10-16 | E-MTAB-8228 | biostudies-arrayexpress

scRNAseq of human iPSC-derived kidney organoids transplanted in the coelomic cavity of chicken embryos compared to untransplanted controls

Project description:Human induced pluripotent stem cell-derived kidney organoids have potential for disease modelling and regenerative medicine purposes. However, they lack a functional vasculature and remain immature in in vitro culture. Here, we transplanted kidney organoids at day 7+12 of differentiation in the coelomic cavity of chicken embryos and then compared them to their respective untransplanted controls at d7+13 and d7+20 using scRNAseq and imaging modalities. We demonstrate vascularization and enhanced maturation of transplanted kidney organoids.

2022-08-05 | E-MTAB-11429 | biostudies-arrayexpress

Single cell RNA sequencing of endometrial organoids in the IVMC protocol

Project description:Accessing endometrial tissue during the early phases of the menstrual cycle is challenging. With this experiment we are capturing the dynamic epithelial cell states after breakdown using endometrial organoids (EOs) subjected to the in vitro menstrual cycle (IVMC) protocol. EOs are collected for scRNAseq analysis before breakdown (Hormonal Withdrawal 48h), 12h after breakdown (Post-breakdown 12h), 24h after breakdown (Post-breakdown 24h), 48h after breakdown (Post-breakdown 48h) as well as 24h (E2 differentiation 24h) and 48h after estrogen treatment (E2 differentiation 48h).

2026-04-28 | E-MTAB-15330 | biostudies-arrayexpress

Transcriptional profiling of mouse molar and incisor tooth organoids

Project description:Organoid models provide powerful tools to study tissue biology and development in a dish. Here, we established first-time organoid models from early-postnatal (postnatal day 7) mouse molar and incisor, capable of differentiation toward ameloblast-like cells in vitro. To more in detail characterise organoids from mouse molar and incisor, bulk RNA-sequencing was performed on the following (1) early passage (passage 0) organoids from both tooth types grown in basal tooth organoid medium (TOM) with or without addition of exogenous epidermal growth factor (EGF); and (2) late passage (passage 5) organoids grown in TOM+EGF or differentiation medium (DM).

2023-04-19 | E-MTAB-12557 | biostudies-arrayexpress

The extracellular function of LGALS3BP in neural progenitors during brain development

Project description:This study demonstrates cellular and molecular mechanisms regulating the generation and function of basal radial glia (bRG), a neural stem cell population that was shown to be enriched in the developing human brain and was involved in the formation of cortical expansion. Here, we studied the role of LGALS3BP, a secreted protein whose RNA expression is enriched in bRGs. Based on a combination of three model systems i) in vitro human cerebral organoids, ii) ex vivo embryonic human fetal tissue and iii) in vivo embryonic mouse cortex, and a wide variety of techniques including single-cell RNA-sequencing, proteomics, and immunostaining, we characterized the role of human LGALS3BP mutations.

2021-05-12 | E-MTAB-10485 | biostudies-arrayexpress

Impact of intermittent lead exposure on hominid brain evolution

Project description:Lead Exposure and Human Brain Evolution: A 2-Million-Year Perspective This study reveals that lead exposure was pervasive throughout human evolution, not just a modern phenomenon. Researchers analyzed 51 fossil teeth from multiple hominid species spanning 2+ million years across three continents, finding lead exposure evidence in 73% of specimens using advanced laser ablation mass spectrometry. The team then used human brain organoids carrying either modern or archaic (Neanderthal-like) variants of the NOVA1 gene to test lead's neurological impacts. They discovered that the archaic variant showed greater vulnerability to lead-induced disruption of FOXP2 expression—a gene crucial for speech and language development. This suggests environmental lead exposure may have created evolutionary pressure favoring the modern human NOVA1 variant, potentially giving our species advantages in communication and social cohesion. The research challenges established paradigms about both environmental toxin history and human evolution, proposing that gene-environment interactions with neurotoxins helped shape our species' cognitive development over millions of years.

2025-10-27 | PXD067623 | Pride

Single cell RNA-seq of great ape cerebral organoids

Project description:The human brain has changed dramatically from other primate species, but the genetic and developmental mechanisms behind the differences remains unclear. Here we used single cell RNA sequencing based on 10X technology to explore temporal transcriptomic dynamics and cellular heterogeneity in cerebral organoids derived from human and non-human primates chimpanzee and rhesus macaque stem cells. Using cerebral organoids as a proxy of early brain development, we detect a delayed pace of human brain development relative to the other two primate species. Additional human-specific gene expression patterns resolved to different cell states through progenitors to neurons are also found. Our data provide a transcriptomic cell atlas of primate early brain development, and illustrate features that are unique to humans.

2019-12-30 | E-MTAB-7552 | biostudies-arrayexpress

RNA-seq of small intestinal organoids treated with the control medium ENR (EGF, Noggin, R-spondin1) in the presence or absence of muscle supernatant

Project description:In order to unravel the impact of intestinal smooth muscle tissue on the intestinal epithelium, we isolated clean smooth muscle, cultured it for 24h in DMEM-F12, and collected the supernatant (muscle-SN). This supernatant was used to treat small intestinal organoids (made of intestinal epithelium), compared to normal ENR treatment. After 5 days of muscle-SN exposure, we disrupted the organoids, and directly isolate the RNA. RNA-seq was performed in this sample to assess the genetic changes induced by muscle products.

2021-09-27 | E-MTAB-9181 | biostudies-arrayexpress

Mosaic perturbation of transcription factors in human retinal organoid development

Project description:To begin to understand how TFs regulate retinal cell type identity in human tissues, we established a pooled loss of function (LOF) experiment based on the CROP-seq protocol in developed retinal organoids. We targeted five TFs (OTX2, NRL, CRX, VSX2, and PAX6) that are important for retinal development and expressed dynamically over the organoid developmental time course.

2023-02-24 | E-MTAB-12622 | 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