Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Robust parameter design of human induced pluripotent stem cell differentiation protocols defines lineage‐specific induction of anterior‐posterior gut tube endodermal cells

ABSTRACT: Robust parameter design of human induced pluripotent stem cell differentiation protocols defines lineage‐specific induction of anterior‐posterior gut tube endodermal cells

PROVIDER: PRJNA685108 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13251062.fastq.gz	Fastqsanger.gz
	SRR13251063.fastq.gz	Fastqsanger.gz
	SRR13251064.fastq.gz	Fastqsanger.gz
	SRR13251065.fastq.gz	Fastqsanger.gz
	SRR13251066.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

Robust parameter design of human induced pluripotent stem cell differentiation protocols defines lineage‐specific induction of anterior‐posterior gut tube endodermal cells

Project description:Tissues and cells derived from pluripotent stem cells (PSC) are likely to become widely used in disease modeling, drug screening, and regenerative medicine. For these applications, the in vitro PSC differentiation process must be elaborately investigated and controlled to reliably obtain the desired end products. However, because traditional experimental methods, such as one factor at a time (OFAT) or brute-force approaches, are impractical for detailed screening of complex PSC cultivation conditions, more strategic and effective screening based on statistical design of experiments (DOE) ought to be indispensable. Among various DOE approaches, we regard robust parameter design (RPD) as particularly suited for differentiation protocol optimization due to its suitability for multi-factorial screening. We confirmed the adaptability of RPD for investigating human induced PSC (hiPSC) lineage specification toward anterior–posterior gut tube endodermal cells and clarified the contribution of each cell signaling pathway and the effect of cell signaling condition alteration on marker RNA expression levels, while increasing the efficiency of the screening in 243-fold (18 vs 4374) compared to that of a brute-force approach. Specific induction of anterior foregut, hepatic, pancreatic, or mid-hindgut cells was achieved using seven iPSC strains with the optimal culture protocols established on the basis of RPD analysis. RPD has the potential to enable efficient construction and optimization of PSC differentiation protocols, and its use is recommended from fundamental research to mass production of PSC-derived products.

2021-01-06 | GSE163148 | GEO

Transcriptional state during endodermal differentiation

Project description:ChIP-seq was performed to determine the transcriptional activity of genes during endodermal differentiation RNA pol II occupancy and histone marks of elongation and gene repression were analyzed during early endodermal differentiation

2012-09-25 | E-GEOD-41111 | biostudies-arrayexpress

Control ChIP-seq from endodermal cell (ENCSR273FER)

Project description:Control ChIP-seq on endodermal cell originated from endodermal cell For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2021-03-29 | GSE170148 | GEO

TF ChIP-seq from endodermal cell (ENCSR398RET)

Project description:CTCF ChIP-seq on endodermal cell originated from endodermal cell For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2021-05-23 | GSE175231 | GEO

PRC2 Promotes Canalisation During Endodermal Differentiation

Project description:PRC2 Promotes Canalisation During Endodermal Differentiation

| PRJNA1208096 | ENA

Free of choice on anterior and posterior chest tube position after lung cancer resection.

Project description:ObjectivesThe optimal location to insert a chest tube for postoperative drainage has not been identified. We performed a retrospective equivalence study to identify whether the efficiency is similar regarding anterior or posterior position of chest tube in thoracic cavity after video-assisted thoracoscopic surgery for non-small-cell lung cancer.MethodsA retrospective review of 4263 patients undergoing non-small-cell lung cancer resection from October 2009 to August 2019 in the Western China Lung Cancer Database was conducted. Propensity score matching was performed to balance baseline characteristics between anterior and posterior groups. Chest tube duration, drainage volume, postoperative complications and hospitalization cost were compared. Equivalence margin was defined as (-1, 1) in 95% confidence interval of the mean difference of chest tube duration.ResultsAfter propensity score matching, we investigated 2912 patients with anterior or posterior (1456 vs 1456) chest tube location following lung cancer resection. The mean time to chest tube removal was 3.39 days in the anterior group and 3.38 days in the posterior group (P = 0.52), while the mean difference and 95% confidence interval were 0.02 (-0.17, 0.20). The mean postoperative hospital stays in 2 groups were 5.47 vs 5.24 days (anterior vs posterior, P = 0.02). No significant differences were identified regarding the drainage volume during the first 3 postoperative days, postoperative complications and hospitalization cost.ConclusionsThe comparison of clinical outcomes between anterior and posterior location of chest tube met the criteria for equivalence. For lung cancer patients undergoing video-assisted thoracoscopic surgery resection, it was free choice on anterior or posterior single-tube insertion.

| S-EPMC9387293 | biostudies-literature

Transcriptional state during endodermal differentiation

Project description:ChIP-seq was performed to determine the transcriptional activity of genes during endodermal differentiation

2012-09-25 | GSE41111 | GEO

Crotonylation of GAPDH regulates human embryonic stem cell endodermal lineage differentiation and metabolic switch

Project description:Post-translational modifications of proteins are crucial to the regulation of their activity and function. As a newly discovered acylation modification, crotonylation of non-histone proteins remains largely unexplored, particularly in human embryonic stem cells (hESCs). Here we report the investigation of induced crotonylation in hESCs, which resulted in hESCs of different pluripotency states differentiating into the endodermal lineage. We showed that increased protein crotonylation in hESCs was accompanied by transcriptomic shifts and decreased glycolysis. Through large-scale profiling of non-histone protein crotonylation, we identified metabolic enzymes as major targets of inducible crotonylation in hESCs. We further discovered GAPDH as a key glycolytic enzyme regulated by crotonylation during endodermal differentiation from hESCs, where crotonylation of GAPDH decreased its enzymatic activity thereby leading to reduced glycolysis. Our study demonstrates that crotonylation of glycolytic enzymes may be crucial to metabolic switching and cell fate determination in hESCs.

2022-10-27 | PXD027007 | Pride

Global RNA expression patterns in endodermal differentiated cells

Project description:This study will analyse the global RNA expression patterns in human iPSC and endodermal differentiated cells.The goal of this project is to investigate genes regulating definitive endodermal differentiation of human iPSC using genetic screening. The differentiation of human iPSC into definitive endoderm is going to be examined by global RNA expression patterns. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2015-06-09 | E-ERAD-363 | biostudies-arrayexpress

Nucleosome occupancy as a novel chromatin parameter for replication origin functions

Project description:This study defines nucleosome occupancy as a novel parameter for regulating origin activities. Nucleosome occupancy at origins was assessed using histone H3 ChIP-seq during G1 and G2M. Origin activity was determined using BrdU ChIP-seq.

2016-11-14 | GSE81028 | 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