Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq for PAX8 and histone modifications in Renal Cell Carcinoma cell lines.

ABSTRACT: In this experiment we analyzed the genome wide occupancy of PAX8 by ChIP-seq in four Renal Cell Carcinoma cell lines. Additionally we performed ChIP-seq also for histone modifications correlated with transcriptional activity (H3K27ac), enhancers (H3K4me1) and promoters (H3K4me3). Unrelated IgG was used as a background noise control.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Swann Gaulis

PROVIDER: E-MTAB-7812 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

BioID of PAX8 in human ovarian cancer cells

Project description:Investigation of interactors for the human transcription factor PAX8 using BioID-based proximity labeling, as described in Galli et al.

2021-03-09 | PXD021709 | Pride

In vitro crosslinking of PAX8 and PRDM3

Project description:MS crosslinking of PAX8 and PRDM3 using standard DSSO-based crosslinking

2021-03-09 | PXD021708 | Pride

Epigenomic remodeling of the PAX8 cistrome in high grade serous ovarian cancer [ChIP-Seq]

2016-08-08 | E-GEOD-79893 | biostudies-arrayexpress

RNA-seq upon PAX8 knockdown in Renal Cell Carcinoma cell lines

Project description:In this experiment we examined the genes regulated by PAX8 knockdown in four renal cell carcinoma models. Four different cell lines bearing a validated doxycycline (DOX) inducible shRNA against PAX8 were treated with DOX for 96 hours and their gene expression profile analyzed by RNA-seq.

2019-06-28 | E-MTAB-7808 | biostudies-arrayexpress

Genome wide profiling of PAX8 binding stes in PCCL3 rat cells

Project description:Analysis of PAX8 binding sites by chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq) in PCCL3 rat cells. Results provide insight into the contribution of this regulatory factor to transcription genome-wide. We generate a genome wide map of PAX8 binding sites in PCCL3 cells using as negative control an input DNA obtained just prior to Pax8 immunoprecipitation

2012-06-27 | E-GEOD-26871 | biostudies-arrayexpress

Gene expression profile changes upon knock-down of Pax8

Project description:In order to define the transcriptional network functionally regulated by Pax8 as well as infer its direct targets, we performed RNAi to knock-down Pax8 gene in FRTL-5 thyroid cells. Expression data from three independent silencing experiments were analyzed by microarray technology unraveling 2815 genes differentially expressed between silenced cells and controls. Of these, 1421 genes were down-regulated and 1394 genes were up-regulated 72hrs after Pax8 silencing. The results obtained suggest that Pax8 regulates numerous pathways, some of which involved in the regulation of cell cycle, thyroid cancer and apoptosis, thus confirming that Pax8 is a master regulatory gene. Rat differentiated thyroid cells from FRTL-5 line were transfected with siGENOME Pax8 siRNA (siPax8, experimental) or siGENOME Non-Targeting siRNA (ntPax8, controls). The trascriptome from three siPax8 biological replicates, 72 hours after transfection, was compared to the trascriptome from 3 control ntPax8 biological replicates. Microarray analysis was performed at gene-level using the AffymetrixGeneChip Rat Gene 1.0 ST array

2011-12-20 | E-GEOD-29341 | biostudies-arrayexpress

Epigenomic remodeling of the PAX8 cistrome in high grade serous ovarian cancer [RNA-Seq]

Project description:We report mapping of the PAX8 cistrome in three high grade serous ovarian cancer cell lines (KURAMOCHI, OVSAHO, and JHOS4) compared to three benign immortalized fallopian tube cell lines (FT33, FT194, and FT246). We identified a highly conserved PAX8 binding pattern common across benign fallopian tube cell lines that was distinct from the unique PAX8 binding patterns seen in each cancer cell line. Comparison of benign and malignant Mullerian cell lines with and without PAX8 knockdown. For each cell line, three distinct siRNAs targeting PAX8 plus a pool of all three siRNAs were examined and compared to both a non-transfected control as well as a control transfected with a non-targeting siRNA.

2016-08-08 | E-GEOD-83100 | biostudies-arrayexpress

ATAC-seq in Renal Cell Carcinoma cell lines

Project description:In this experiment we profiled the genome wide chromatin accessibility in 4 Renal Cell Carcinoma cell lines.

2019-06-28 | E-MTAB-7844 | biostudies-arrayexpress

Lineage factor-dependent signalling by kidney cancer-associated genetic alteration

Project description:As shown by large-scale human genetic data, cancer mutations display strong tissue-selectivity, but how this selectivity arises remains unclear. Here, using experimental models, functional genomics and analysis of patient samples, we demonstrate that the lineage transcription factor paired box 8 (PAX8) is required for oncogenic signalling by two common clear cell renal cell carcinoma (ccRCC)-causing genetic alterations in humans: the germline variant rs7948643 at 11q13.3 and somatic inactivation of the von Hippel-Lindau tumour suppressor (VHL). VHL loss, observed in ~90% of ccRCCs, can lead to hypoxia-inducible factor 2 alpha (HIF2A) stabilization. We show that HIF2A is preferentially recruited to PAX8-bound transcriptional enhancers, including a pro-tumorigenic cyclin D1 (CCND1) enhancer that is controlled by PAX8 and HIF2A. The ccRCC protective allele C at rs7948643 inhibits PAX8 binding at this enhancer and downstream activation of CCND1 expression. Co-option of a PAX8-dependent physiological programme that supports proliferation of normal renal epithelial cells is also required for MYC expression from the ccRCC metastasis-associated amplicons at 8q21.3-q24.3. These results demonstrate that transcriptional lineage factors are essential for the expression of canonical oncogenes and they mediate tissue-specific cancer risk associated with somatic and inherited genetic variants

2022-03-14 | PXD029522 | Pride

PAX8 transcriptional profiling in rat PCCL3 cells

Project description:PAX8 transcriptional profiling of rat PCCL3 cells comparing wild type cells with PAX8 silenced cells and scramble treated with PAX8 silenced cells

2012-06-28 | GSE26937 | 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