Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

EasyPairedTag: A Comprehensive Pipeline for Paired-Tag Data Quality Control and Analysis

ABSTRACT: Paired-Tag is an ultra-high throughput single-cell method for simultaneous profiling of gene expression and histone modifications, enabling identification of cell-type-specific cis-regulatory elements and correlation of their chromatin states with the expression levels of putative target genes. However, the lack of an automated end-to-end pipeline has limited its application. Here, we present easyPairedTag, a Snakemake pipeline for Paired-Tag data processing and quality control. Key features include flexible configuration for diverse experimental setups, automated sub-library merging and sample demultiplexing, and comprehensive quality control metrics. When applied to published mouse brain datasets, easyPairedTag improves overlapping gene quantification via strand-specific analysis for precise cell clustering. In mouse hypothalamus datasets, easyPairedTag is compatible with the processing of paired-end sequencing data to detect histone modification peaks with higher sensitivity and specificity, facilitating the discovery of putitive cell-type-specific cis-regulatory elements.

ORGANISM(S): Mus musculus

PROVIDER: GSE300580 | GEO | 2025/08/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Drosophila melanogaster

Project description:damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets

| PRJNA284767 | ENA

Spatially Resolved Transcriptomics Exploration in 3D Desktop and Virtual Reality Environments with VR-Omics 

Project description:Spatially resolved transcriptomics (SRT) produces complex, multi-dimensional gene expression data sets at up to subcellular spatial resolution. While SRT provides powerful datasets to probe biological processes, well-designed computational tools provide the key to extracting value from SRT technology. Currently, no single piece of software facilitates the combined automated analysis, visualisation, and subsequent interaction of single or multi-section SRT data as a desktop application or in an immersive environment. Here we present VR-Omics, a freely available, SRT platform agnostic, stand-alone programme that incorporates an in-built, automated workflow to pre-process and spatially mine SRT data within a user-friendly graphical interface. Benchmarking demonstrates VR-Omics has superior capabilities for seamless end-to-end analyses of SRT data, hence making SRT data processing and mining accessible to users regardless of computational and data handling skills. Importantly, VR-Omics supports comparison between datasets generated using different spatial technologies alongside processing and analysis of multiple 2D or 3D SRT datasets provides a unique environment for biological discovery. Finally, we utilise VR-Omics to uncover the molecular mechanisms that drive the growth of rare paediatric cardiac rhabdomyomas.

2025-04-22 | GSE252228 | GEO

Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [ChIP-Seq]

Project description:For ATAC-seq data processing, we used the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/). In detail, for each sample, ATAC-seq reads were first checked for adaptor contamination. Then, adaptor trimmed reads were aligned to hg19 using Bowtie2 under paired-end mode with parameter “-X2000”, which permits 2000 bp for the maximum allowable insert size between two paired ends of each read. Using the ENCODE ATAC-seq pipeline, duplicated reads were properly filtered out. ATAC-seq enriched peaks were called using MACS2 (Zhang et al., 2008) based on remaining unique reads with parameters “-f BAMPE -q 0.05 --nomodel”. In total, we collected 45,569 peaks for the ARID1AWT sample and 27,480 peaks for the ARID1AKO sample.

2020-06-08 | GSE106660 | GEO

RNA sequencing analysis of unchallenged, PBS injected and S. pneumoniae infected pcsk9 KO and WT zebrafish

Project description:Purpose: S. pneumoniae infection in both zebrafish larvae and adult fish can be used to model pneumococcal bacteremia. Here, we used unchallenged, PBS injected and S. pneumoniae (T4) infected adult zebrafish to study the genome-wide role of pcsk9 in vivo in steady-state and upon immune system stimulation. Methods: Adult pcsk9 KO zebrafish and their WT siblings were infected with S. pneumoniae (3,370,000 CFU; SD 840,000 CFU) and their total liver RNA isolated at 1-day post infection. RNA-sequencing data was produced by NovaSeq. Data processing pipeline was built on Snakemake wrappers, and used STAR to quantify features from quality and adapter trimmed reads in gene level. Prior to the normalisation and differential gene expression analysis with DESeq2, the matrix of raw gene counts was prefiltered to keep only rows that have at least 10 reads total and then split by treatment to analyze each case separately. Result tables were annotated with biomaRt. Results: Snakemake preprocessing pipeline measured 32,520 genes against GRCz11, ENSEMBL release 97. 20,709 of them was used for statistical testing. Full result tables for each treatment were ranked by p-value and the normalized DESeq2 abundances in samples were included. The genes with BH-adjusted p-value <0.05 was considered differentially expressed. Conclusions: Our study identified up- and down-regulated genes in unchallenged, PBS injected and pneumococcal infected pcsk9 KO zebrafish liver compared to WT zebrafish.

2021-07-02 | GSE165508 | GEO

RNA-seq of H929 cells treated with Solamargine against untreated controls

Project description:To investigate the effects of Solamargine (SM) on multiple myeloma (MM), here we employed RNA-sequencing experiment to explore the transcriptomic response of SM in H929 cells. RNA was extracted from two groups of samples, 3 samples of each, processing as follows: one was treated with a certain volume of SM, and the another was blank control. A total of 6 paired-end RNA-seq datasets were obtained eventually.

2021-08-23 | E-MTAB-10816 | biostudies-arrayexpress

Gene expressions data of Multiple Sclerosis stages, Clinical Isolated Syndrome and healthy controls

Project description:Clinically Isolated Syndromes (CIS)represent the first clinical episode of an inflammatory demyelinating disorder suggestive of MS. Most CIS will develop relapsing-remitting MS (RR), characterized by clinical and inflammatory attacks followed by periods of recovery and stability. With time, most RR-MS subjects will evolve to secondary progressive MS (SP), with advancing neurological impairment in absence of recognizable relapses. A small fraction of MS subjects experience worsening of neurologic function from the onset and are thus defined primary progressive MS (PP). We analysed PBMC transcriptomes relative to 41 healthy subjects, 47 CIS, 49 RR, 22 SP and 27 PP patients and applied a semi-automated pipeline in R Bioconductor platform to perform preprocessing and differential expression analysis.

2023-01-31 | E-MTAB-11415 | biostudies-arrayexpress

CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

Project description:We performed Chromatin Interaction Analysis by Paired-End-Tag sequencing to elucidate CTCF-mediated long range interactions. 1,480 cis and 336 trans interacting loci were identified with high reproducibility. Associating these chromatin interaction loci with histone marks, RNA Pol II, p300 and Lamin B genome wide profiles, we uncover five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and may influence proper gene expression through extensive crosstalk between promoters and regulatory elements.

2011-06-23 | GSE28247 | GEO

Absence of the proprotein convertase FURIN in naive CD8+ T cells modifies the transcriptome of the cells

Project description:Purpose: FURIN is a member of the proprotein convertase subtilisin/kexin (PCSK) family of serine endoproteases important in converting immature proproteins into their functional form. While FURIN is important in various aspects of the immune response such as in CD4+ T cells, FURIN´s role in CD8+ T cells is unclear. Here, we isolated naive CD8+ T cells from conditional T cell specific Furin KO (Cd4-Cre-Furinflox/flox) and WT (Furinflox/flox) mice and studied the genome-wide gene expression pattern using RNA sequencing. Methods: Total RNA was isolated from the naive CD8+ T cells and the RNA-sequencing data was produced by the Finnish Functional Genomics Centre of Turku Bioscience (University of Turku, Turku, Finland) using Illumina HiSeq 2000. Data processing pipeline was built on Snakemake wrappers, and used STAR to quantify features from quality and adapter trimmed reads in gene level. Prior the normalisation and differential gene expression analysis with DESeq2, the matrix of raw gene counts was prefiltered to keep only rows that have at least 10 reads total. Result tables were annotated with biomaRt. Results: Snakemake preprocessing pipeline measured 55573 genes against GRCm38, ENSEMBL release 97. 15843 of them was used for statistical testing. Full result tables for each treatment were ranked by p-value and the normalized DESeq2 abundances in samples were included. The genes with BH-adjusted p-value <0.05 was considered differentially expressed. Conclusions: Our study revealed that the abscence of FURIN from the naive CD8+ T cells causes an effector-like phenotype in comparison to the WT cells.

2023-04-28 | GSE186812 | GEO

Zebrafish Paired End DiTag libraries

Project description:Used a DNA tag sequencing and mapping strategy called gene identification signature (GIS) analysis, in which 5' and 3' signatures of full-length cDNAs are accurately extracted into paired-end ditags (PETs) that are concatenated for efficient sequencing and mapped to genome sequences to demarcate the transcription boundaries of every gene. GIS analysis is potentially 30-fold more efficient than standard cDNA sequencing approaches for transcriptome characterization. Keywords: Paired End DiTags

2008-12-01 | GSE6694 | GEO

Paired end protocol test

Project description:Paired end protocol test

| PRJEB2279 | ENA