Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-seq experiment in two versions of Raji cells with inducible BZLF1 variants prior to and after induction of EBV's lytic cycle by doxycycline.

ABSTRACT: The aim of the experiment was to identify accessible (open) chromatin regions in the genome prior to and post induction of EBV's lytic phase by the BZLF1 protein. Two versions of BZLF1 were employed: full-length and activation-domain (AD)-truncated BZLF1 non-induced and induced for 15 h. The experiments were performed as triplicates.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Homo sapiens

SUBMITTER: Alexander Buschle

PROVIDER: E-MTAB-7789 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ATAC-seq analyses with results from DG75 cells prior to and post induction of two versions of BZLF1.

Project description:The aim of the experiment was to identify accessible (open) chromatin regions in the genome prior to and post induction of EBV's BZLF1 protein. Two versions of BZLF1 were employed: full-length and activation-domain (AD)-truncated BZLF1 non-induced and induced for 15 h. The experiments were performed as triplicates.

2021-02-07 | E-MTAB-8420 | biostudies-arrayexpress

Identification of chromatin interactions of 49 selected cellular loci prior to and post induction of BZFL1 in DG75 cells using the Capture-C technology.

Project description:Identification of specific chromatin interactions of 49 selected genes with the Capture-C technique in DG75 iBZLF1 cells prior to and 15 h after expression of EBV's protein BZLF1. The experiments were performed as triplicates.

2021-02-07 | E-MTAB-8427 | biostudies-arrayexpress

ChIP-seq data from DG75 cells with the BZLF1 specific antibody BZ1

Project description:ChIP-seq experiments with the antibody BZ1 directed against the EBV protein BZLF1 prior to and 15 hours post induction with doxycycline (100 ng/ml). The doxycycline regulated conditional BZLF1 allele is encoded by an inducible oriP plasmid vector stably introduced into DG75 cells. Experiments were performed as duplicates.

2021-02-07 | E-MTAB-8422 | biostudies-arrayexpress

RNA-seq data from DG75 cells with inducible BZLF1 prior to and after induction of EBV's lytic cycle by doxycycline.

Project description:(i) Transcripts of DG75 iBZLF1 cells were analyzed comparing non-induced cells and cells induced with doxycycline (100 ng/ ml) for 6 h. Doxycycline induces the expression of the full length viral transcription factor BZLF1. (ii) For control purposes, the transcripts of DG75 cells equipped with a doxycycline-regulated truncated BZLF1 allele lacking its transactivation domain (DG75 iBZLF1 AD-truncated) were analyzed prior to and after induction with doxycycline for 6 h. (iii) For an additional control, the transcripts of parental, unmodified DG75 cells were analyzed prior to and after adding doxycycline for 6 h. All experiments were performed as triplicates. The analysis is based on Homo sapiens (human) genome assembly GRCh37 (hg19) from Genome Reference Consortium. Artificial ERCC Spike-in RNAs (Thermo Scientific) were added as external controls.

2021-02-07 | E-MTAB-8426 | biostudies-arrayexpress

ChIP-seq against BZLF1 in Raji cells (EBV, Human Herpesvirus 4, GenBank accession KF717093).

Project description:ChIP-seq experiments with the antibody BZ1 directed against the EBV protein BZLF1 prior to and 15 hours post induction with doxycycline (100 ng/ml). The doxycycline regulated conditional BZLF1 allele is encoded by an inducible plasmid stably introduced into Raji cells. Experiments were performed as duplicates.

2019-04-01 | E-MTAB-7788 | biostudies-arrayexpress

Single cell transcriptomics of irradiated colorectal cancer organoids

Project description:Single cell RNA sequencing of two colorectal organoid lines that were irradiated plus their controls

2022-06-26 | E-MTAB-11849 | biostudies-arrayexpress

Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities

Project description:Histone deacetylases (HDACs) have been widely pursued as targets for anti-cancer therapeutics. However, many of these targets are universally essential for cell survival, which may limit the therapeutic window that can be achieved by drug candidates. By examining large collections of CRISPR/Cas9-based essentiality screens, we discovered a genetic interaction between HDAC1 and HDAC2 wherein each paralog is synthetically lethal with hemizygous deletion of the other. This collateral synthetic lethality is caused by recurrent chromosomal translocations that occur in diverse solid and hematological malignancies, including neuroblastoma and multiple myeloma. Using genetic deletion or dTAG-mediated degradation, we show that HDAC2 disruption suppresses the growth of HDAC1-deficient neuroblastoma in vitro and in vivo. Mechanistically, we find that targeted degradation of HDAC2 in these cells prompts the degradation of several members of the nucleosome remodeling and deacetylase (NuRD) complex, leading to diminished chromatin accessibility at HDAC2/NuRD-bound sites of the genome and impaired control of enhancer-associated transcription. Furthermore, we reveal that several of the degraded NuRD complex subunits are dependencies in neuroblastoma and multiple myeloma, providing motivation to develop paralog-selective HDAC1 or HDAC2 degraders. Altogether, we identify HDAC1/2 collateral synthetic lethality as a new therapeutic target and reveal a novel mechanism for exploiting NuRD-associated cancer dependencies.

2023-06-11 | PXD034444 | Pride

An improved TurboID-based proximity labeling pipeline in C. elegans by biochemical depletion of endogenously biotinylated carboxylases

Project description:To review an improved proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes, the interactome of a presynaptic active zone protein, ELKS-1, was analyzed as proof of principle. A significant constraint on the sensitivity of TurboID-based proximity labeling is the presence of abundant, endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a co-factor. We developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry, by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography (IMAC).

2022-09-12 | PXD034639 | Pride

Single-cell sequencing of HEK293FT cells with molecular spikes and recorded cell size

Project description:Individual HEK cells were dispensed using an F.SIGHT into individual wells while recording cell diameters. Each well contained 0.0321 pg of molecular spike-ins, a highly complex set of 264 molecular spikes, based on 11 unique spike sequences spanning different lengths (570 to 3070 nts) and GC contents (40-60%). Libraries were generated with Smart-seq3xpress protocol.

2022-02-16 | E-MTAB-11433 | biostudies-arrayexpress

Multisystem inflammatory syndrome in children (MIS-C) serum proteomics

Project description:While fewer cases of severe Coronavirus Disease 2019 (COVID-19) are reported globally in children, a small proportion of SARS-CoV-2 infected children develop a novel pediatric febrile entity called multisystem inflammatory syndrome in children (MIS-C) that develops 2 to 5 weeks after initial SARS-CoV-2 exposure. MIS-C primarily effects male children and children of Hispanic or black descent. MIS-C manifests as a severe and uncontrolled inflammatory response with multiorgan involvement. A hyperinflammatory state is evidenced by clinical makers of inflammation including high levels of C-reactive protein (CRP), ferritin, and D-dimers, and an increased expression of pro-inflammatory cytokines. Children often present with persistent fever, severe gastrointestinal symptoms, cardiovascular manifestations, respiratory symptoms and neurological symptoms6-11,13. Cardiovascular manifestations include hypotension, shock, cardiac dysfunction, myocarditis and pericardial effusion. In the united states, admission to the intensive care unit occurs in approximately 58% of cases. To understand disease pathogenesis of MIS-C and proteins associated with the severe form of disease we performed proteomics analysis of serum or plasma samples. We collected serum from healthy children (SARS-CoV-2 negative, n=20), mild MIS-C (non-ICU, n=5) and severe MIS-C (ICU, n = 20) patients. MIS-C definition and diagnosis was performed according to CDC guidelines. Healthy adult serum (n = 4) was also used for reference ranges quality control and we obtained plasma samples from Kawasaki Disease (KD; n=7) patients that were recruited before the Coronavirus Disease 2019 (COVID-19) pandemic.

2021-09-29 | PXD025462 | Pride

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