Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PRC1.6 ChIPseq - mouse ES

ABSTRACT: Components of the PRC1.6 complex were depleted via Crisper/Cas9 and ChIPed in mouse ES cells.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Mus musculus

SUBMITTER: Bastian Stielow

PROVIDER: E-MTAB-6007 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

PRC1.6 ChIPseq - HEK239

Project description:Components of the PRC1.6 complex were depleted via Crisper/Cas9 and ChIPed in HEK293 cells.

2018-01-24 | E-MTAB-6006 | biostudies-arrayexpress

PRC1.6 RNAseq

Project description:MGA was depleted via Crisper/Cas9 in HEK293 cells and the resulting gene expression changes were profiled.

2018-01-24 | E-MTAB-6005 | biostudies-arrayexpress

A combined genomic approach unveils the transcriptional basis of heterogeneity of human pancreatic ductal adenocarcinoma [RNA-seq]

Project description:The histological grade of carcinomas describes the ability of tumor cells to organize differentiated epithelial structures and has prognostic impact. Molecular control of differentiation in normal and cancer cells relies on lineage-determining transcription factors (TFs) that activate the repertoire of cis-regulatory elements controlling cell type-specific transcriptional outputs. TF recruitment to cognate genomic DNA binding sites results in the deposition of histone marks characteristic of enhancers and other cis-regulatory elements. Here we integrated transcriptomics and genome-wide analysis of chromatin marks in human pancreatic ductal adenocarcinoma (PDAC) cells of different grade to identify first, and then experimentally validate the sequence-specific TFs controlling grade-specific gene expression. We identified a core set of TFs with a pervasive binding to the enhancer repertoire characteristic of differentiated PDACs and controlling different modules of the epithelial gene expression program. Defining the regulatory networks that control the maintenance of epithelial differentiation of PDAC cells will help determine the molecular basis of PDAC heterogeneity and progression. Poly(A) fraction of the total RNA from human pancreatic ductal adenocarcinoma cell lines was extracted and subjected to by multiparallel sequencing. Experiments were carried out in unmodified cells in duplicate, genome edited clonal CFPAC1 cells (2 KLF5-deleted CRISPR-Cas9 clones, 3 ELF3-deleted CRISPR-Cas9 clones and 2 wt clones) and CFPAC1 cells ectopically expressing ZEB1 or empty vector control (in duplicate).

2016-01-18 | E-GEOD-64558 | biostudies-arrayexpress

A combined genomic approach unveils the transcriptional basis of heterogeneity of human pancreatic ductal adenocarcinoma.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-01-18 | E-GEOD-64560 | biostudies-arrayexpress

RNA-Seq of mouse embryonic stem cells derived from genetically diverse inbred mouse strains with varying alleles at Lifr gene

Project description:We measured genome-wide gene expression of embryonic stem cells derived from two different inbred mouse genetic backgrounds. For each genetic background we also conducted an allele swap at SNP rs50454566 upstream of the Lifr gene. We profiled cells from each of the four strains in triplicate (technical replicates). We cultured cells in media with LIF + GSK3-beta inhibitor CHIR99021. Cells remained unfed until harvest, six days later.

2020-08-13 | E-MTAB-8695 | biostudies-arrayexpress

TCF/LEF dependent and independent regulation of Wnt/beta-catenin transcription

Project description:During canonical Wnt signalling the activity of nuclear beta-catenin is largely mediated by the TCF/LEF family of transcription factors. To challenge this view we used the CRISPR/Cas9 genome editing approach to generate HEK 293T cell clones simultaneously carrying loss-of-function alleles of all four TCF/LEF genes. Exploiting unbiased whole transcriptome sequencing studies, we found that a subset of beta-catenin transcriptional targets did not require TCF/LEF factors for their regulation. Consistent with this finding, we observed in a genome-wide analysis that beta-catenin occupied specific genomic regions in the absence of TCF/LEF. Finally, we revealed the existence of a transcriptional activity of beta-catenin that specifically appears when TCF/LEF factors are absent, and refer to this as beta-catenin-GHOST response. Collectively, this study uncovers a previously neglected modus operandi of beta-catenin that bypasses the TCF/LEF transcription factors.

2018-11-02 | E-MTAB-7029 | biostudies-arrayexpress

Transcriptome profiling of MED1 wild-type and knockout human pre-B ALL cell line 697 (RNA-seq)

Project description:CRISPR/Cas9 system was used to generate mediator complex subunit 1 (MED1) knockout human pre-B ALL cell line 697. RNA-seq was performed to observe the effects of MED1 deletion on gene expression in 697.

2020-05-13 | E-MTAB-8178 | biostudies-arrayexpress

DNA-microarray of human breast cancer cell line MCF10A harboring PSD4 knock-out and wild-type control

Project description:To address the mechanism of action of EFA6B we have knocked-out its gene PSD4 using the CRISPR/Cas9 technology. The MCF10A human mammary cell line was used for the knock-out as it is a well-characterized normal human mammary cell line and thus enabled us to study the effect of deleting PSD4 in a non-transformed genetic background.

2021-03-01 | E-MTAB-10063 | biostudies-arrayexpress

Genome-wide profiling of MED1 and RUNX1 binding in MED1 wild-type and knockout human pre-B ALL cell line 697 (ChIP-seq)

Project description:CRISPR/Cas9 system was used to generate mediator complex subunit 1 (MED1) knockout human pre-B ALL cell line 697. ChIP-seq was performed to identify genomic regions responsible for recruitment of MED1 and RUNX1.

2020-05-13 | E-MTAB-8177 | biostudies-arrayexpress

Transcription profiling of human adenocarcinoma cell line A549 over-expressing ELMOD2

Project description:ELMOD2 cDNA from the IMAGE clone 3897166 was cloned into the pDsRed-Monomer-N1 expression vector. ELMOD2 was overexpressed in the A549(adenomcarcinoma)cell line and cells transfected with empty vector were considered controls. Transcript profiles were compared with the Affymetrix Hgu133plus2 arrays. Three biological replicates of each condition were included.

2009-12-07 | E-MEXP-1838 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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