Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation (ChIP-Seq)

PROVIDER: PRJNA173869 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR547548.fastq.gz	Fastqsanger.gz
	SRR547549.fastq.gz	Fastqsanger.gz
	SRR547550.fastq.gz	Fastqsanger.gz
	SRR547551.fastq.gz	Fastqsanger.gz
	SRR547552.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9

Similar Datasets

Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation

Project description:Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation

| PRJNA168155 | ENA

Homo sapiens

Project description:Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation (Human)

| PRJNA168174 | ENA

Rattus norvegicus

Project description:Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation (Rat)

| PRJNA168175 | ENA

RNA-seq analysis of 2 cell line models of lung disease (A549 and BEAS-2B) and primary bronchial epithelial cells in Project 3 of Open Targets 020 - Epigenomes of Cell Lines

Project description:This experiment captures the baseline expression of two cell lines (A549, BEAS-2B) selected for Project 3, Open Targets 020 (http://opentargets.org). These cell lines are both possible models for lung disease. In addition, the baseline expression of bronchial epithelial primary cells (NHBE cells) from 3 donors has also been measured. <br> This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalized cell lines/models. This signature will be used in combination with data from ChIP-seq experiments from the same cell lines against primary cells and tissues. The overall aim of the Open Targets Cell Line Epigenome project is to establish a systematic approach for the determination of human biological and disease relevance through the generation of transcriptomic and epigenomic data in cell lines of interest. Comparison of cell line mRNA expression and epigenome data with existing and newly generated reference data from human tissue and cell types will identify assay systems that will provide greater confidence in translating target biology and compound pharmacology to patients.

2017-07-04 | E-MTAB-4729 | biostudies-arrayexpress

INTEGRATED MULTI-OMICS ANALYSIS OF PBX1 IN MOUSE ADULT NEURAL STEMAND PROGENITOR CELLS IDENTIFIES A TRANSCRIPTIONAL MODULE WITH RELEVANCE TO LEUKEMOGENESIS

Project description:Developmental transcription factors act in networks, but how these networks achieve cell- and tissue specificity is still poorly understood. We here explored pre-B-cell leukemia homeobox 1 (PBX1) in adult neurogenesis combining genomic, transcriptomic, and proteomic approaches. ChIP-Seq analysis uncovered PBX1 binding to a wide range of different genes. Integration of PBX1 ChIP-seq with ATAC-seq data predicted interaction partners, which were subsequently validated by mass-spectrometry. Spatial transcriptomics revealed distinct temporal expression dynamics of Pbx1 and interacting factors. Among these were class I bHLH proteins TCF3, TCF4 and TCF12. RNA-seq upon Pbx1, Tcf3 and Tcf4 knockdown identified proliferation and differentiation associated genes as shared targets. Neuronal differentiation was reduced upon depletion of either factor, suggesting functional cooperation between PBX1 and TCF3/4. Notably, while physiological PBX1-TCF interactions have not yet been described, chromosomal translocation resulting in genomic TCF3::PBX1 fusion characterizes a subtype of acute lymphoblastic leukemia. Introducing Pbx1 into Nalm6 cells, a pre B-cell line expressing TCF3 but lacking PBX1, upregulated leukemogenic genes including BLK and NOTCH3, arguing that functional PBX1-TCF cooperation likely extends to hematopoietic contexts. Our study hence uncovers a PBX1-TCF module orchestrating the balance between progenitor cell proliferation and differentiation in adult neurogenesis with implications for leukemia etiology.

2024-09-16 | PXD048222 | Pride

Integrated epigenomic and transcriptomic profiling of terminal human erythropoiesis [ATAC-seq]

Project description:Integrated epigenomic and transcriptomic profiling of terminal human erythropoiesis [ATAC-seq]

| PRJNA475744 | ENA

Integrated epigenomic and transcriptomic profiling of terminal human erythropoiesis [RNA-seq]

Project description:Integrated epigenomic and transcriptomic profiling of terminal human erythropoiesis [RNA-seq]

| PRJNA475757 | ENA

The epigenomic landscape of cognitive stimulation in the context of aging in mouse dorsal hippocampus - SWATH

Project description:Aging is a universal biological phenomenon linked to many diseases, such as cancer or neurodegeneration. However, the molecular mechanisms underlying aging, or how lifestyle interventions such as cognitive stimulation can ameliorate this process, are yet to be clarified. Here, we performed a multi-omic profiling, including RNA-seq, ATAC-seq, ChIP-seq, EM-seq, SWATH-MS and single cell Multiome scRNA and scATAC-seq, in the dorsal hippocampus of young and old mouse subjects which were subject to cognitive stimulation using the paradigm of environmental enrichment. In this study we were able to describe the epigenomic landscape of aging and cognitive stimulation.

2023-09-29 | PXD045567 | Pride

BrainSpan Atlas of the Human Brain

Project description:<p>The NIH-funded BrainSpan (<a href="http://www.brainspan.org/" target="_blank">www.brainspan.org</a>) and PsychENCODE (<a href="http://development.psychencode.org" target="_blank">www.psychencode.org</a>). Consortia sought to generate and analyze multi-dimensional genomics data from the developing and adult human brain in healthy and disease states. One of the main goals has been to perform large-scale and integrated analysis of the genome, transcriptome, and epigenome of the human brain to broaden our understanding of human neurodevelopment. This dataset consists of sixteen regions, including eleven neocortical areas, of human donors of both sexes and various ethnic groups. In the first stage of this project, we provide the genome-wide exon-level transcriptome data generated using the Affymetrix GeneChip Human Exon 1.0 ST Arrays, and the genome-wide genotyping data for 2.5 million markers using the Illumina Human Omni 2.5-Quad Bead Chips. In the second stage of this project, we provide whole-genome sequencing data, transcriptome data by mRNA-Seq, small RNA data by smRNA-seq, DNA cytosine methylation by Infinium HumanMethylation450 BeadChip, and epigenomic/epigenetic data by ChIP-Seq for H3K4me3, H3K27me3, H3K27ac and CTCF.</p>

| phs000755 | dbGaP

Homo sapiens

Project description:MacroH2A1 ChIP-seq from IMR90 human primary lung fibroblasts

| PRJNA237811 | ENA