Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

55 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CUT&RUN of HOXA6 and HOXB6 in neuronal-derived human embryonic stem cells

ABSTRACT: CUT&RUN analysis of HOXA6 and HOXB6 binding sites in neuronal-derived human embryonic stem cells

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Shay Kinreich

PROVIDER: E-MTAB-13627 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

CUT&RUN of Sox2 binding in the mouse P0 visual thalamus (dLGN)

Project description:CUT&RUN was performed for Sox2 on ex-vivo dissected visual thalamic nuclei from P0 mice, revealing context specific activity of Sox2 binding in differentiated neurons.

2023-06-03 | E-MTAB-13004 | biostudies-arrayexpress

CUT&RUN experiment in colon cancer cells (HCT116, DLD1 and SW620), assessing TBX3 genomic occupancy

Project description:The Wnt/β-catenin signaling pathway plays crucial roles in nearly all parts of embryonic development and adult stem cell homeostasis. Its aberrant activation has been linked to many diseases such as developmental irregularities and various severe forms of cancer, with colorectal cancer (CRC) as a prime example. While much work has been dedicated to uncovering effective therapeutics to block oncogenic Wnt signaling, such interventions have not proven trivial because of the broad activity of Wnt throughout the adult body and the difficulty in finding suitable molecular targets. We have previously identified the developmental transcription factor TBX3 as a participant of the Wnt-mediated transcriptional regulation. Here we examine the genome-wide binding pattern of TBX3 in the human CRC cells lines HCT116 (25 replicates), DLD1 (2 replicates) and SW620 (2 replicates), by employing CUT&RUN (C&R) with Low-Volume and Urea (LoV-U; Zambanini et al., 2022).

2024-01-01 | E-MTAB-13646 | biostudies-arrayexpress

STAT1 and IRF1 enrichment in naive and primed HeLa cells upon IFNγ treatment

Project description:STAT1 and IRF1 transcription factor enrichment by CUT&RUN. HeLa cells were primed with IFNγ for 24 hours, followed with IFNγ washout. After 48h, naïve and primed cells were induced by IFNγ for 1h and 3h. Cells were harvested at indicated time points and processed for CUT&RUN

2023-05-06 | E-MTAB-12625 | biostudies-arrayexpress

CUT&RUN LoV-U of H3K4me3, b-catenin, and IgG in HCT116 cells

Project description:We performed high numbers of replicates of CUT&RUN LoV-U against H3K4me3, β-catenin, and the negative control IgG in human colorectal cancer HCT116 cells over two independent rounds of experiments to discover the complete set of binding events.

2023-07-21 | E-MTAB-13143 | biostudies-arrayexpress

Genome-wide analysis of histone modifications in latently HIV-1 infected T cells

Project description:The epigenetic mechanisms established by histone modifications may affect the transcriptional silencing of HIV-1 and viral latency. A systematic epigenome profiling could be applicable to develop new epigenetic diagnostic markers for detecting HIV-1 latency. In this study, histone modification profiles of HIV-1 latency cell lines were compared with those of uninfected CD4+ T cell line. The HIV-1 latency gave rise to differential histone modification regions. The differential enrichment patterns helped us to define potential effector genes leading to the viral latency. The histone H3K4me3 and H3K9ac profiles were obtained from the HIV-1 latency cell lines (NCHA1, NCHA2, and ACH2) and control CD4+ T cell line (A3.01)

2014-06-06 | E-GEOD-58247 | biostudies-arrayexpress

CutnRun directed against O-GlcNac in the human DLD-1 cell line with doxycycline treatment to induce RNA Polymerase II degradation

Project description:This experiment aimed at investigating how O-GlcNac occupancy sites are impacted by RNA Polymerase II removal upon doxycycline stimulation. These human colon adenocarcinoma DLD-1 cells express OsTIR and a cassette encoding mini-AID (mAID) and fluorescent protein mClover (mAID+mClover) at the initiation site of the endogenous Rpb1 gene locus (POLR2A) (Nagashima 2019).

2024-08-31 | E-MTAB-14307 | biostudies-arrayexpress

The exon junction complex is restricted to a specific subset of splice junctions

Project description:We employ multi-step affinity purification followed by high-throughput sequencing to determine the location of EJC complexes assembled on a cellular transcriptome in Drosophila S2 cells, finding 6% of the intron-containing genes were not associated with EJCs, and within genes with multiple introns, only specific exon-exon junctions assembled an EJC. RIP-Seq, 3 samples

2014-11-04 | E-GEOD-33475 | biostudies-arrayexpress

RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [ChIP-seq]

Project description:ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism, and reveal different mechanisms at two different promoter architectures. Genomic localization of RSC, ISW1a, and SWI/SNF complexes were measured by chromatin immunoprecipitation followed by Illumina paired-end sequencing. Four strains were analyzed, including Rsc8-9xMyc (YBC2882), Sth1-2xFlag (YBC601 p3018), Ioc3-13xMyc (YBC2883), and Snf2-13xMyc (YBC3010). Each sample consists of one chromatin immunoprecipitate and one input chromatin control.

2015-04-01 | E-GEOD-65592 | biostudies-arrayexpress

CutnRun of O-GlcNac in mouse ES cells in high glucose condition

Project description:Study of the chromatin occupancy of O-GlcNac in mouse ES cells cultivated in a high glucose concentration media

2024-08-31 | E-MTAB-14308 | biostudies-arrayexpress

CutnRun of O-GlcNac in mouse ES cells in low glucose condition at 6 hours, 8 hours, and 1 week

Project description:Study of the chromatin occupancy of O-GlcNac in mouse ES cells cultivated in low glucose condition at 6 hours, 8 hours, and 1 week

2024-08-31 | E-MTAB-14309 | biostudies-arrayexpress

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