Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

104 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Benchmarking brain organoid recapitulation of fetal corticogenesis

ABSTRACT: Brain organoids (BO) enabled the investigation of human corticogenesis in-vitro with an increasing range of protocols achieving its remarkable recapitulation. However, we lack a resource gathering fetal cortex-specific gene co-expression patterns and their behavior in BO. We complement the current knowledge with a benchmarking of BO versus human corticogenesis, integrating: transcriptomes from in-house differentiated cortical BO (CBO), in-house processed human fetal brain samples, analysis of transcriptomes from different BO systems and of pre-natal cortical samples from the BrainSpan Atlas.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-11239 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP134351

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Cationic amino acid transporter-1 influences the leptin transport in an iPSC-derived in vitro blood-brain barrier model

Project description:Total RNAs extracted from iPSC-derived BMEC-like cells with or without 17β-estradiol treatment were collected and analyzed using RNA sequencing.

2022-05-16 | E-MTAB-11691 | biostudies-arrayexpress

Human iPSC-derived cardiomyocytes of peripartum cardiomyopathy patients reveal aberrant expression of sterol and lipid metabolism pathways

Project description:To identify the consequences of mechanical stress of differentiated cardiac muscles from healthy- and PPCM individuals. RNA-sequencing data was obtained from 4 individuals from 2 families. Each family had one member with PPCM and one healthy. Individual 1 and 2 were sisters, one healthy, one with PPCM. Individual 3 and 4 were a healthy mother and PPCM daughter. From each patient 4, 6, 1 and 3 clones were derived, respectively. From each clone multiple pairs of cells were collected and either stretched or left static to a total of 40 pairs, with 2 unpaired static samples.

2020-12-08 | E-MTAB-9053 | biostudies-arrayexpress

3'SRP data of cardiac differentiation of human induced pluripotent stem cell control lines

Project description:Human heart development is governed by transcription factor (TF) networks controlling dynamic and temporal gene expression alterations. Therefore, to comprehensively characterize these transcriptional regulations, day-to-day transcriptomic profiles were generated throughout the directed cardiac differentiation, starting from three distinct human induced pluripotent stem cell lines from healthy donors (32 days).

2022-12-06 | E-MTAB-11822 | biostudies-arrayexpress

Reactive astrocytes transduce blood-brain barrier inflammation through a TNFα-STAT3 signaling axis and secretion of alpha 1-antichymotrypsin

Project description:Total RNAs extracted from iPSC-astrocytes or iPSC-BMEC like cells grown together or separately in transwells were collected and analyzed using RNA sequencing. In addition, total RNAs extracted from conditions with or without TNF-a were analyzed.

2022-03-05 | E-MTAB-11468 | biostudies-arrayexpress

RNA-seq of Immortalized cardiac cell lines for characterization and comparison

Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.

2021-10-06 | E-MTAB-10720 | biostudies-arrayexpress

Immortalized cardiac cell line characterization and comparison (mouse/mouse-derived)

2022-01-04 | E-MTAB-10912 | biostudies-arrayexpress

Immortalized cardiac cell line characterization and comparison (rat/rat-derived)

2022-01-04 | E-MTAB-10913 | biostudies-arrayexpress

scRNA-seq to investigate endoderm differentiation from induced human pluripotent stem cells

Project description:Single-cell RNA-seq (scRNA-seq) on nocodazole and DMSO treated cells before and after differentiation into endoderm. hPSC colonies were treated with DMSO or 100ng/ml nocodazole for 16 hours and induced to differentiate into definitive endoderm for three days. Single cells were subsequently collected in either undifferentiated conditions (Und) or after 3 days of endoderm differentiation (Endoderm) and then sorted onto 384 well plates for Smart-Seq2 processing.

2019-02-09 | E-MTAB-7008 | biostudies-arrayexpress

Human pluripotent stem cell-derived ROR1e lens epithelial cell single cell RNA-sequencing

Project description:Detailed transcriptomic analyses of differentiated cell populations derived from human pluripotent stem cells is routinely used to assess the identity and utility of the differentiated cells. In particular, single cell RNA-sequencing (scRNA-seq) can provide insights into both the cellular and transcriptional heterogeneity of differentiated cell populations. Here we provide scRNA-seq data obtained from ROR1-expressing lens epithelial cells (ROR1e LECs) obtained via directed differentiation of CA1 human embryonic stem cells. Through the use of principal component analysis, heat maps and gene ontology assessments, we demonstrate that ROR1e LECs represent a highly purified and large-scale population of lens cells. These data provide a resource for future characterisation of both normal and cataractous human lens biology.

2020-11-27 | E-MTAB-9178 | biostudies-arrayexpress

An in vivo neuroimmune organoid model to study human brain environment-dependent microglia phenotypes

Project description:Characterization of human stem cell-derived microglia (hMG) that develop within vascularized human brain organoids under physiological conditions in vivo. We isolated tdT+/CD45+ hMG from five animals and three time points (6, 12 and 24 weeks post transplantation) using Fluorescence-activated cell sorting (FACS), following a strictly controlled ex vivo isolation procedure as previously described (Gosselin et al., 2017) and profiled those cells using single cell RNA sequencing.

2023-05-11 | E-MTAB-11522 | 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