Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of brain organoids from human NKX2.1(GFP/w) hESCs treated with patterning molecules

ABSTRACT: RNA-seq of brain organoids from human NKX2.1(GFP/w) hESCs treated with patterning molecules

PROVIDER: PRJEB42820 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR5216750_1.fastq.gz	Fastqsanger.gz
	ERR5216750_2.fastq.gz	Fastqsanger.gz
	ERR5216760_1.fastq.gz	Fastqsanger.gz
	ERR5216760_2.fastq.gz	Fastqsanger.gz
	ERR5216770_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 120

Similar Datasets

RNA-seq of brain organoids from human NKX2.1(GFP/w) hESCs treated with patterning molecules

Project description:There are on-going efforts to steer brain organoid development toward distinct regional identities by supplying cues in defined culture conditions. Here we incubated developing organoids with a number of patterning molecules at different concentrations to assess their effects on establishing brain region identities.

2021-02-11 | E-MTAB-10037 | biostudies-arrayexpress

Total RNA sequencing of INS-GFP+ cells differentiated from HES3 hESCs treated with DMSO or H1152

Project description:To systematically examine the cellular identity of INS+ cells derived after H1152 treatment, INSw/GFP HES3 hESCs were differentiated to a pancreatic progenitor population and treated with 10 µM H1152 for 8 days in sphere culture. The INS-GFP+ cells of H1152 or DMSO treated spheres were purified by cell sorting and transcripts profiled using RNA-seq.

2017-07-01 | GSE84325 | GEO

Transcription profiling by array of human NKX2.1GFP/w spin embryoid bodies differentiated and then FACS sorted based on FORSE-1, NKX2.1-GFP and PDGFR expression

Project description:The gene targeted NKX2.1GFP/w hESC line was differentiated as spin EBs in BPEL medium supplemented with FGF2 and retinoic acid to generate NKX2.1-GFP+ neural cells. NKX2.1-GFP+ cells were FACS sorted and further differentiated in serum free BEL medium supplemented with FGF2 (20 ng/ml) and EGF1 (20 ng/ml) on laminin-coated flasks. After ~ 90 days in culture, cells were FACS sorted based on FORSE-1 and NKX2.1-GFP expression, with the FORSE-1-GFP- fraction further fractionated on the basis of PDGFR? expression. Sorted fractions were subjected to Illumina microarray processing.

2011-01-05 | E-MEXP-2808 | biostudies-arrayexpress

KW-2449 and VPA exert therapeutic effects on human neurons and cerebral organoids derived from MECP2-null hESCs

Project description:To gain a deeper insight into roles of MECP2 in hESCs derived organoids, we performed RNA-seq to analyze the transcriptome changes after MECP2 deletion in hESCs-derived organoids.

2022-10-08 | GSE214885 | GEO

Examination of the role of BMP signaling in patterning of human pluripotent stem cell derived mid/hindgut spheroids and maintenance of this patterning in organoids transplanted under mouse kidney capsules.

Project description:The goal of this study was to test the hypothesis that BMP signaling regulates patterning of human CDX2+ gut tube cultures (Spence et al 2011, Watson et al. 2014). The study is comprised of 2 separate experiments. The first experiment was to determine the immediate impact of BMP signaling on CDX2+ gut tube cultures. To do so we tested spheroids, spheroids after plating in Matrigel and exposed to 3 days of Noggin (100ng/mL), spheroids after plating in Matrigel and exposed to 3 days of EGF alone (100ng/mL, Control), and spheroids after plating in Matrigel and exposed to 3 days of BMP2 (100ng/mL). RNA was collected from spheroids and spheroids after 3 days of patterning. The second experiment examined if patterning was maintained after this initial 3 days of patterning and an addition 8-10 weeks following transplantation in vivo. To do this we grew all Matrigel plated spheroids for an additional 25 days in media containing EGF alone (Control media). We then transplanted these organoids under the mouse kidney capsule and allowed them to mature for 8-10 weeks. We then collected RNA from the transplanted organoids.

2017-04-20 | E-MTAB-5658 | biostudies-arrayexpress

Expression data from GFP control and GFP-PRDM1 transduced H9 hESCS

Project description:The mechanisms of transcriptional regulation underlying human primordial germ cell differentiation are largely unknown. Transcriptional repressor Prdm1/Blimp1 is known to play a critical role in controlling germ cell specification in mice. We show that ectopic expression of PRDM1 in hESCs promotes the generation of cells exhibiting transcriptomic features of early primordial germ cells.

2016-12-11 | GSE53283 | GEO

Using hESCs to Probe the Interaction of CDKAL1 and MT1E, Two GWAS identified Diabetes Associated Genes

Project description:We report the RNA expression of insulin-GFP+ cells derived from CDKAL1-/- hESCs and CDKAL1-/-hESCs overexpressing MT1E

2017-07-01 | GSE97591 | GEO

RNAseq of GFP-sorted cells (Low-GFP vs. High-GFP, GFP-fed vs GFP+fed)

Project description:RNAseq of GFP-sorted cells (Low-GFP vs. High-GFP, GFP-fed vs GFP+fed)

| PRJNA544322 | ENA

Comparison non-targeting hRNA hESCs versus UBE2K shRNA hESCs

Project description:Histones modulate gene expression by chromatin compaction, regulating numerous processes such as differentiation. However, the mechanisms underlying histone degradation remain elusive. When compared with their differentiated counterparts, immortal human embryonic stem cells (hESCs) have a unique chromatin architecture and low levels of trimethylated histone H3 at lysine 9 (H3K9me3), a heterochromatin-associated modification. Here we assess a link between the intrinsic epigenetic landscape and ubiquitin-proteasome system of hESCs. We find that hESCs exhibit high expression of UBE2K, a ubiquitin-conjugating enzyme. Loss of UBE2K increases the levels of H3K9 trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation. Concomitantly, loss of UBE2K impairs the ability of hESCs to differentiate into neural progenitors with neurogenic properties. Besides H3K9 trimethylation, we find that UBE2K binds histone H3 to induce its polyubiquitination and degradation by the proteasome. Notably, ubc-20, the worm orthologue of UBE2K, also regulates both histone H3 levels and H3K9 trimethylation in C. elegans germline. Thus, our results indicate that UBE2K crosses evolutionary boundaries to promote histone H3 degradation and reduce H3K9me3 repressive marks in immortal cells.

2020-06-01 | PXD018625 | Pride

Gene expression in human embryonic stem cells (hESCs) upon the differentiation to neural lineages by timed delivery of retinoic acid

Project description:We report gene-expression profiling of hESCs differentiating to neuronal lineages upon the treatment with Retinoic Acid and Smoothened Agonisnt. We study weather RA patterning activity relies on duration of RA exposure and can be used to direct differentiation of hESCs into distinct neuronal cell types.

2020-08-31 | GSE147404 | GEO

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