Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pasha: a versatile R package for piling chromatin HTS data

ABSTRACT: We describe an R package designed for processing aligned reads from chromatin-oriented high-throughput sequencing experiments. Pasha (preprocessing of aligned sequences from HTS analyses) allows easy manipulation of aligned reads from short-read sequencing technologies (ChIP-Seq, FAIRE-seq, Mnase-Seq...) and offers innovative approaches to process and extract relevant information.

ORGANISM(S): Homo sapiens

PROVIDER: GSE79385 | GEO | 2016/03/18

SECONDARY ACCESSION(S): PRJNA315673

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome analysis of Human Trophoblast Stem cell (HTS) and TEAD4 knock down HTS cells by next generation sequencing

Project description:mRNA profiles of control Human Trophoblast Stem cell (HTS) and TEAD4 knock down HTS cells were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000 platform. TEAD4 Knock down in HTS cells were confirmed by RT-PCR analysis and immuno staining.

2020-05-29 | GSE144809 | GEO

Spatially patterned scaffolds enhances vascular organization and functional integration in volumetrc muscle loss

Project description:We report the application of bioengineered skeletal muscle composed of murine skeletal myoblasts interspersed with human vascular endothelial cells (ECs) using spatially patterned scaffolds for the treatment of volumetric muscle loss. To gain insights into the molecular mechanisms by which spatial patterning promoted myo-angiogenesis, we performed mRNA sequencing of engineered muscle and endothelialized engineered muscle on either randomly-oriented or aligned scaffolds. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from four groups: 1) randomly-oriented scaffold seeded with myoblasts; 2) randomly-oriented scaffolds seeded with myoblasts + ECs; 3) aligned scaffold seeded with myoblasts only; 4) aligned scaffold seeded with myoblasts + ECs. Samples were generated in triplicate and the NovaSeq 6000 (Illumina) sequencing platform was utilized. 150-bp paired-end reads were generated (20-30 million reads per sample). The raw data were checked for quality with FastQC (Version 0.11.7) and results were aggregated with MultiQC and were aligned to the mouse genome (GRCm38) using STAR (Version 2.5.3a) with ENCODE options for long RNA-seq pipeline. The alignment results were assessed using Samtools and aggregated with MultiQC (Version 1.5) and the differential gene expression analysis of the uniquely mapped reads/raw counts wwas performed using the DESeq2 package (Version 1.20.0). Each DE analysis was composed of a pairwise comparison between an experimental group and the control group. Differentially expressed genes were identified after false discovery rate (FDR = 0.05) correction.

2019-04-01 | GSE127171 | GEO

Enhancing Tendon Regeneration: Investigating the Impact of Topography on the Secretome of Adipose-Derived Stem Cells

Project description:Proteomic analysis based on the inbuilt label-free quantification (LFQ) was conducted to examine the secretome of ADSCs cultured on randomly oriented or aligned silk scaffolds for 24h. ultured on randomly oriented or aligned silk scaffolds for 24h.

2023-12-13 | PXD047809 |

Homo sapiens

Project description:Pasha: a versatile R package for piling chromatin HTS data

| PRJNA315673 | ENA

Barcodes from HTS data

Project description:HTS data as a source of diatom barcode sequences

| PRJEB27890 | ENA

Small Molecule Inducers of Neuroprotective miR-132 Identified by HTS-HTS in Human iPSC-derived Neurons

Project description:MicroRNAs (miRNAs) are short RNAs that regulate fundamental biological processes. miR-132, a key miRNA with established functions in Tau homeostasis and neuroprotection, is consistently downregulated in Alzheimer’s disease (AD) and other tauopathies. miR-132 overexpression rescues neurodegenerative phenotypes in several AD models. To complement research on miRNA-mimicking oligonucleotides targeting the central nervous system, we developed a high-throughput-screen coupled high-throughput-sequencing (HTS-HTS) in human induced pluripotent stem cell (iPSC)-derived neurons to identify small molecule inducers of miR-132. We discovered that cardiac glycosides, which are canonical sodium-potassium ATPase inhibitors, selectively upregulated miR-132 in the sub-μM range. Coordinately, cardiac glycoside treatment downregulated total and phosphorylated Tau in rodent and human neurons and protected against toxicity by glutamate, N-methyl-D-aspartate, rotenone, and Aβ oligomers. In conclusion, we identified small-molecule drugs that upregulated the neuroprotective miR-132 and ameliorated neurodegenerative phenotypes. Our dataset also represents a comprehensive resource for discovering small molecules that modulate specific miRNAs for therapeutic purposes.

2023-10-19 | GSE216991 | GEO

Identification of TEAD4 target genes in Human trophoblast stem cells (HTS) by ChIP-seq analysis.

Project description:ChIP-seq profiles of TEAD4 and input in Human trophoblast stem cells (HTS) using Illumina NovaSeq 6000 Sequencing System.

2020-05-29 | GSE144807 | GEO

Barcode sequences from HTS data

Project description:HTS data as a source of diatom barcode sequences

| PRJEB27918 | ENA

Small Molecule Inducers of Neuroprotective miR-132 Identified by HTS-HTS in Human iPSC-derived Neurons

Project description:Small Molecule Inducers of Neuroprotective miR-132 Identified by HTS-HTS in Human iPSC-derived Neurons

| PRJNA896539 | ENA

Topography-dependent gene expression in migratory glioma cells

Project description:The goal of this experiment was to compare the gene expression of glioma cells migrating on substrates of different topographies and to determine a migration-associated gene profile. Human malignant glioma U251MG cells were cultured on highly-aligned versus randomly-oriented electrospun nanofibers of poly-caprolactone. Cells migrated actively on aligned nanofibers but motility was very restricted on randomly-oriented fibers. Results of gene expression profiling indicated upregulation of a JAK/STAT signature in actively migrating glioma cells. Total RNA was extracted from 3 independent cultures of U251 glioma cells cultured on aligned versus random nanofibers and applied to Affymetrix HG-U133 plus 2 chips. Analysis of gene expression was used to determine a gene-signature correlated with different substrate topography

2011-03-24 | E-GEOD-28167 | 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