Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

VDR ChIP-Seq on colonic human organoids

ABSTRACT: VDR ChIP-Seq on colonic human organoids

PROVIDER: PRJNA419552 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6317760.fastq.gz	Fastqsanger.gz
	SRR6317761.fastq.gz	Fastqsanger.gz
	SRR6317762.fastq.gz	Fastqsanger.gz
	SRR6317763.fastq.gz	Fastqsanger.gz
	SRR6317764.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

VDR ChIP-Seq on colonic human organoids

Project description:Genome-wide maps of VDR binding sites in colonic organoids estimulated with calcitriol

2019-07-21 | GSE107283 | GEO

Vitamin D receptor (VDR) ChIP-Seq on human colonic organoids stimulated with 1,25(OH)2D3

Project description:Genome-wide VDR chromatin binding sites in colonic organoids stimulated with 1,25(OH)2D3 for 2h.

2024-07-01 | GSE206176 | GEO

Vitamin D receptor (VDR) ChIP-Seq on human colonic organoids stimulated with 1,25(OH)2D3

Project description:Vitamin D receptor (VDR) ChIP-Seq on human colonic organoids stimulated with 1,25(OH)2D3

| PRJNA849561 | ENA

Organoids-on-a-chip for Colorectal Cancer and in Vitro Screening of Chemotherapeutic Drugs

Project description:The individualized treatment of tumors has always been an urgent problem in clinical practice. Organoids-on-a-chip can reflect the heterogeneity of tumors and is a good model for in vitro anticancer drug screening. In this study, surgical specimens of patients with advanced colorectal cancer will be collected for organoid culture and organoids-on-a- chip. Use organoids-on-a-chip to screen tumor chemotherapy drugs, compare the results of patients’ actual medication regimens, and study the guiding role of organoids in the formulation of precise tumor treatment plans. The investigators will compare the response of organoids to drugs in vitro with the patient’s response to actual chemotherapy and targeted drugs and explore the feasibility and accuracy of organoids-on-a-chip based drug screening for advanced colorectal cancer. The project will establish a screening platform for chemotherapeutic drugs and targeted drugs based on colorectal cancer organoids to quickly and accurately formulate personalized treatment plans for clinical patients.

| 2385953 | ecrin-mdr-crc

1,25(OH)D3 effect on colonic organoids from wt and VDR KO mice

Project description:1,25(OH)D3 effect on colonic organoids from wt and VDR KO mice

| PRJNA414728 | ENA

Transcriptomics of cytokine-treated human colonic epithelial organoids

Project description:Mapping of transcriptional changes elicited by cytokines mediating canonical immune responses in human colonic organoids

2022-08-08 | GSE190634 | GEO

Genomic and epigenomic 1α,25(OH)2D3 responses in human colonic organoids

Project description:Background & Aims: Active vitamin D, 1α,25(OH)2D3, is a nuclear hormone with roles in colonic homeostasis and carcinogenesis, yet mechanisms underlying these effects are incompletely understood. Human organoids are an ideal system to study genomic and epigenomic host-environment interactions. Here, we utilize human colonic organoids to measure 1α,25(OH)2D3 responses on genome-wide gene expression and chromatin accessibilityover time. Methods: Human colonic organoids were cultured and treated in triplicate with either 100nM 1α,25(OH)2D3 or vehicle control for 4 and 18 hours (h) for chromatin accessibility, and 6 and 24hfor gene expression. DNA and RNA were extracted for ATAC- and RNA-sequencing, respectively. Differentially accessible peaks were analyzed using DiffBind and EdgeR; differentially expressed genes were analyzed using DESeq2. Motif enrichment was determined using HOMER. Results: At 6h and 24h, 2870 and 2721 differentially expressed genes, respectively (FDR<5%) were identified with overall stronger responses with 1α,25(OH)2D3. Similarly, 1α,25(OH)2D3 treatment led to stronger chromatin accessibility especially at 4h. The vitamin D receptor (VDR) motif was strongly enriched among open chromatin peaks with 1α,25(OH)2D3 treatment accounting for 30.5% and 11% of target sequences at 4h and 18h, respectively (FDR<1%). A number of genes such as CYP24A1, FGF19, MYC, FOS and TGFBR2 showed significant transcriptional and chromatin accessibility responses to 1α,25(OH)2D3 treatment with open chromatin located distant from promoters for some gene regions. Conclusions: Assessment of chromatin accessibility and transcriptional responses to 1α,25(OH)2D3 yielded new observations about vitamin D genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study host-environment interactions between individuals and populations in future.

2020-12-09 | GSE162856 | GEO

Transcriptional profiling of colonic Regulatory T (Treg) cells, CD4+ conventional T (Tconv) cells, dendritic cells (DCs), and epithelial cells (ECs) from Vdr WT- or Vdr KO-Foxp3 reporter mice

Project description:We reported transcriptional characterization of Treg cells, Tconv cells, and DCs isolated from coloinc lamina propria of Vdr WT- or Vdr KO-Foxp3 reporter mice. We also reported transcriptional characterization of colonic ECs isolated from Vdr WT- or Vdr KO-Foxp3 reporter mice.

2019-12-31 | GSE137405 | GEO

Transcriptomics of IL9 and IL13-treated human colonic epithelial organoids

Project description:Mapping of transcriptional changes elicited by cytokines mediating Th2 and Th9 responses in human colonic organoids

2022-08-08 | GSE190705 | GEO

Genomic and epigenomic responses to aspirin in human colonic organoids

Project description:Background & Aims: Aspirin (ASA) is a proven chemoprotective agent for colorectal cancer; yet, mechanisms underlying these effects are incompletely understood. Human organoids are an ideal system to study genomic and epigenomic host-environment interactions. Here, we utilize human colonic organoids to profile ASA responses on genome-wide gene expression and chromatin accessibility. Methods: Human colonic organoids from one individual were cultured and treated in triplicate with 3mM ASA or vehicle control (DMSO) for 24 hours. Gene expression and chromatin accessibility were measured using RNA- and ATAC-sequencing, respectively. Differentially expressed genes were analyzed using DESeq2. Gene set enrichment was performed by SetRank. Differentially accessible peaks were analyzed using DiffBind and EdgeR. Motif enrichment was determined using HOMER and diffTF. Results: The results yielded strong transcriptional responses to ASA treatment with significant enrichment for fatty acid oxidation and PPAR signaling in the normal colonic epithelium that were validated in independent organoid lines. A large number of differentially accessible chromatin regions were found in response to ASA treatment with significant enrichment for Fos, Jun and Hnf transcription factor motifs. Integrated analysis of epigenomic and genomic treatment responses highlighted genes and regulatory regions that could mediate ASA’s specific effects in the colon including those involved in chemoprotection and/or toxicity. Conclusions: Assessment of chromatin accessibility and transcriptional responses to ASA yielded new observations about genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study colonic ASA responses between individuals and populations in future.

2023-01-01 | GSE198434 | 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