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

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RUNX2)

ABSTRACT: The aim of the experiment was to explore the RUNX2 genomic functions in the papillary thyroid carcinoma. To this end, we performed Chromatin Immunoprecipitation followed by deep-sequencing using an antibody against RUNX2 in TPC1 thyroid cancer cell line, in order to define the genomic regions bound by this transcription factor.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Federica Torricelli

PROVIDER: E-MTAB-11051 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RNA-POLII)

Project description:We performed Chromatin Immunoprecipitation followed by deep-sequencing in TPC1 thyroid cancer cell line model, in order to identify the genomic elements enriched in RNA-Polymerase II, the enzymatic complex required for gene transcription. These data were integrated with RUNX2 genomic occupancy to map the RUNX2 responsive elements that are actively transcribed.

2023-10-20 | E-MTAB-11052 | biostudies-arrayexpress

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq Histone Markers)

Project description:We performed Chromatin Immunoprecipitation followed by deep-sequencing in TPC1 thyroid cancer cell line model, in order to profile the genomic distribution of H3K27ac, H3K4me1 and H3K4me3, epigenetic markers of chromatin functional status. These data were integrated with RUNX2 genomic occupancy to define the nature and the activation status of the RUNX2-associated regions.

2023-10-20 | E-MTAB-11050 | biostudies-arrayexpress

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach

Project description:The aim of this experiment was to identify the RUNX2-dependent transcriptional program in thyroid cancer. To this end TPC1 cell line was infected with dCas9-KRAB and sgRNA targeting RUNX2 distal promoter or a non-targeting sgRNA as control. RNA was collected 10 days after infection and changes in gene expression were evaluated by mRNA-seq. Three replicates were analyzed.

2023-10-20 | E-MTAB-11049 | biostudies-arrayexpress

RNA-seq of thyroid cancer cell line upon silencing of RAIN, a RUNX2 associated intergenic lncRNA, and RUNX2

Project description:The aim of this experiment was to identify the RUNX2- and RAIN-dependent transcriptional program in thyroid cancer. TPC1 and MDA-T41 cell line were infected with dCas9-KRAB and sgRNA targeting the gene of interest (RAIN or RUNX2 respectively) or a non-targeting (NT) sgRNA as control. RNA was collected 10 days after infection and changes in gene expression were evaluated by total RNA-seq.

2024-09-12 | E-MTAB-13777 | biostudies-arrayexpress

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RUNX2)

Project description:Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RUNX2)

| PRJEB48248 | ENA

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach

Project description:Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach

| PRJEB48247 | ENA

Papillary thyroid cancer cell lines treated with Y15

Project description:3 papillary thyroid cancer cell lines were compared, treated with Y15 to untreated. 1 million cells of each papillary thyroid cell line (TPC1, K1, BCPAP) were plated, treated 24 hours later with 10uM Y15, and collected 24 hours later by trypsinization.

2014-03-06 | E-GEOD-55603 | biostudies-arrayexpress

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RNA-POLII)

Project description:Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq RNA-POLII)

| PRJEB48250 | ENA

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq Histone Markers)

Project description:Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach (ChIP-seq Histone Markers)

| PRJEB48249 | ENA

Altered gene expression by hsa_circ_0000839 in papillary thyroid cancer cells

Project description:The expression level of hsa_circ_0000839 was downregulated in papillary thyroid cancer. However, its functions were still unclear. To explore the functions of hsa_circ_0000839, we analyzed the gene expression in TPC1 cells with or without hsa_circ_0000839 silencing.

2020-11-05 | GSE160796 | 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