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

ATAC-seq in neuroblastoma IMR-32 cell line

ABSTRACT: ATAC-seq to define open chromatin in the neuroblastoma IMR-32 cell line.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Bieke Decaesteker

PROVIDER: E-MTAB-6562 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ATAC-seq in IMR-32, CLB-GA and SH-EP neuroblastoma cell lines.

Project description:ATAC-seq to define open and closed chromatin in the human IMR-32, CLB-GA and SH-EP neuroblastoma cell lines in an untreated way.

2023-02-23 | E-MTAB-12588 | biostudies-arrayexpress

ATAC-seq of human CLB-GA neuroblastoma cell line with SOX11 knockdown as compared to control

Project description:ATAC-seq to define open and closed chromatin in the human CLG-GA neuroblastoma cell line upon SOX11 knockdown using siRNAs. Analysis was performed 48h upon after nucleofection, control samples are treated with siNTC (non-targeting control). 2 biological replicates were used.

2023-12-30 | E-MTAB-9463 | biostudies-arrayexpress

Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (ATAC-Seq - iPSCs [N])

Project description:Cornelia de Lange syndrome (CdLS) is a rare genetic disease associated with cohesinopathy. A novel iPSC line was generated from the CdLS patient carrying a heterozygous missense point-mutation of the NIPBL gene. iPSC lines prepared from the healthy parents and the mutation-corrected isogenic cell lines are used as the respective controls. Upon differentiation into hepatocytes, the patient-derived iPSC demonstrate the capacity to express hepatocyte-specific marker transcripts and the respective proteins, however, the efficiency of differentiation is significantly inferior to those of the respective controls, demonstrated by single-cell RNA sequencing and immune-fluorescent analyses. Global change of transcriptome in the patient-derived iPSC relative to the control cells is associated with altered chromatin accessibility, assessed by RNAseq combined with ATACseq analysis. Differentially down-regulated genes in the patient-derived iPSC, in particular, are those coding for proteins related to neural differentiation and transcription factors, while up-regulated genes contain some of antisense RNA coding genes, pseudo genes and long non-coding RNAs. Some of the differentially regulated genes are consistent with the altered chromatin accessibility and this observation is consistent during hepatocyte differentiation. Thus, the mutation in the NIPBL gene of the CdLS patient could be responsible for defects of differentiation primarily due to alteration of chromatin accessibility.

2023-11-01 | E-MTAB-13240 | biostudies-arrayexpress

Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (ATAC-Seq - D9)

2023-06-23 | E-MTAB-12684 | biostudies-arrayexpress

Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (ATAC-Seq - D22)

2023-06-15 | E-MTAB-12661 | biostudies-arrayexpress

ATAC-seq to investigate rewiring the transcriptome of castration-resistant prostate cancer through CDK9 inhibition dataset 1

Project description:The rewiring of transcriptional and epigenetic programs is a hallmark of cancer and a targetable vulnerability for treating metastatic cancers. CDK9, whose primary function is to promote transcriptional elongation at active gene promoters, is emerging as a therapeutic target with broad efficacy in various cancer types. We used the novel and selective CDK9 inhibitor PRT2527 to demonstrate this approach's therapeutic efficacy and tolerability in multiple preclinical tumor models with specific transcriptional dependencies. In castration-resistant prostate cancer (CRPC), PRT2527 inhibited CDK9, AR and other transcription factors (e.g., c-MYC, STAT3, and NF-B) implicated in disease progression and treatment resistance. PRT2527 reduced the proliferation of tumor cell lines and the growth of 3D tumor organoids and spheroids, demonstrating the impact on the bulk tumor cells and the stem-like subpopulation in human and murine CRPC models. PRT2527 was also highly active in vivo in patient-derived CRPC models LuCaP 35 and LuCap 145.2) and transgenic Pb-Cre4;Ptenflox/flox;R26ERG (ERG/PTEN) mice. Notably, PRT2527 induced relevant changes in gene expression, reflecting the impact on the distinct transcriptional programs of various CRPC models. Despite this heterogeneity, a common core of genes and pathways related to oncogenesis was affected in all models. Our data further demonstrate the efficacy and safety of CDK9 inhibition in multiple models of transcriptionally addicted solid tumors. Given its role in transcription, CDK9 is an ideal target for developing novel therapeutic strategies to block tumor cell plasticity driving tumor progression, metastatic spread, and treatment resistance.

2026-04-08 | E-MTAB-12986 | biostudies-arrayexpress

scGET-seq profile of NIH-3T3 cells with Kdm5c knockdown

Project description:scGET-seq profiling of NIH3T3 cells in which Kdm5c was silenced with antisense shRNA or with a control scramble shRNA.

2021-08-17 | E-MTAB-9651 | biostudies-arrayexpress

Determining open chromatin profiles of a specific population of cells isolated from zebrafish embryos at 10 hours post fertilization using the ATAC-seq method

Project description:Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer (10.7554/eLife.03848). Specifically, the 2.7 kb Mouse Smarcd3-F6 sequence (chr5: 24113559 -24116342 from mm9 assembly) was sub-cloned from a gateway entry vector into the Zebrafish Enhancer Detection (ZED). Tol2-mediated transgenesis was performed and stable lines were created. The Smarcd3-F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3-F6:EGFPhsc70 embryos were dissociated at 10 hours post fertilization for fluorescent activated cell sorting (FACS). 30,000-50,000 GFP positive and negative cells were collected from FACS for ATAC-seq. ATAC-seq libraries were created with Tn5 transposase and single-end sequenced on the Illumina HiSeq 2500 platform

2018-08-21 | E-MTAB-6078 | biostudies-arrayexpress

Epigenetic profile of iPSC differentiation process by scGET-seq

Project description:Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scGET-seq.

2021-08-17 | E-MTAB-9649 | biostudies-arrayexpress

Epigenetic profile of iPSC differentiation process by scGET-seq

Project description:Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scGET-seq.

2021-08-17 | E-MTAB-10218 | 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