Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LRGASP challenge WTC11 ssCAGE sequencing derived peaks

ABSTRACT: LRGASP challenge WTC11 ssCAGE sequencing derived peaks

PROVIDER: PRJNA771361 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16340033.fastq.gz	Fastqsanger.gz
	SRR16340034.fastq.gz	Fastqsanger.gz
	SRR16340035.fastq.gz	Fastqsanger.gz
	SRR16340036.fastq.gz	Fastqsanger.gz
	SRR16340037.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

LRGASP challenge WTC11 ssCAGE sequencing derived peaks

Project description:The LRGASP challenge encompasses different human, mouse, and manatee samples sequenced using multiple combinations of protocols and platforms. Different challenges will use distinct subsets of the samples for evaluation. The long-read sequencing platforms used in these challenges are the Pacific Biosciences (PacBio) Sequel II, Oxford Nanopore (ONT) MinION and PromethION. Samples will also be sequenced on the Illumina HiSeq 2500. The primary LRGASP library prep protocols are “standard” cDNA sequencing, direct RNA sequencing, R2C2, and CapTrap. Each sample will also include Lexogen SIRV-Set 4 spike-ins. We will also provide simulated PacBio and ONT data as part of the evaluations. This particular study focuses on single strand CAGE sequencing of human iPSCs, defining CAGE peaks from Illumina HiSeq 2500 (SR: 150 cycles) of two biological replicates for use in the LRGASP challenge.

2021-10-27 | GSE185917 | GEO

BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks

Project description:BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks

| PRJNA543507 | ENA

CUT&Tag recovers up to half of ENCODE ChIP-seq peaks

Project description:We comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Across a total of 30 new and 6 published CUT&Tag datasets we found that no experiment recovers more than 50% of known ENCODE peaks, regardless of the histone mark. We tested peak callers MACS2 and SEACR, identifying optimal peak calling parameters. Balancing both precision and recall of known ENCODE peaks, SEACR without retention of duplicates showed the best performance. We found that reducing PCR cycles during library preparation lowered duplication rates at the expense of ENCODE peak recovery. Despite the moderate ENCODE peak recovery, peaks identified by CUT&Tag represent the strongest ENCODE peaks and show the same functional and biological enrichments as ChIP-seq peaks identified by ENCODE. Our workflow systematically evaluates the merits of methodological adjustments and will facilitate future efforts to apply CUT&Tag in human tissues and single cells.

2022-03-31 | GSE199611 | GEO

ac4C-RIP-seq to identify mRNA ac4C peaks

Project description:ac4C-RIP-seq to identify mRNA ac4C peaks

| PRJNA941324 | ENA

BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks

Project description:We present a tool for processing NGS DNA-seq BAM files to quantify peaks and create coverage tracks from ChIP-seq, NS-seq, ATAC-seq, OK-seq, END-seq and replication timing data

2020-05-17 | GSE131417 | GEO

Detecting differential peaks in ChIP-seq signals with ODIN

Project description:Motivation: Detection of changes in DNA-protein interactions from ChIP-seq data is a crucial step in unraveling the regulatory networks behind biological processes. The simplest variation of this problem is the differential peak calling problem. Here one has to find genomic regions with ChIP-seq signal changes between two cellular conditions in the interaction of a protein with DNA. The great majority of peak calling methods can only analyse one ChIP-seq signal at a time and are unable to perform differential peak calling. Recently, a few approaches based on the combination of these peak callers with statistical tests for detecting differential digital expression have been proposed. However, these methods fail to detect detailed changes of protein-DNA interactions. Results: We propose ODIN; an HMM-based approach to detect and analyse differential peaks in pairs of ChIP-seq data. ODIN performs genomic signal processing, peak calling and p-value calculation in an integrated framework. We also propose an evaluation methodology to compare ODIN with competing methods. The evaluation method is based on the association of differential peaks with expression changes in the same cellular conditions. Our empirical study based on several ChIP-seq experiments from transcription factors, histone modifications and simulated data shows that ODIN outperforms considered competing methods in most scenarios. H3K4me1 and PU.1 occupancy in MPP, CDP, cDC and pDC

2015-01-07 | E-GEOD-57563 | biostudies-arrayexpress

Active Promoters give rise to false positive 'Phantom Peaks' in ChIP-Seq experiments

Project description:We applied ChIP-seq to map the chromosomal binding sites for two nucleosome remodeling complexes containing the ATPase ISWI, ACF and RSF, in Drosophila embryos. Employing a panel of polyclonal and monoclonal antibodies directed against their signature subunits, ACF1 and RSF1, robust profiles were obtained indicating that both remodelers co-occupied a large set of active promoters. For further validation we repeated the mapping using chromatin of mutant embryos that do not express ACF1 or RSF1. Surprisingly, the ChIP-seq profiles were unchanged, suggesting that they were not due to specific immunoprecipitation. Conservative analysis lists about 3000 chromosomal loci, mostly active promoters that are prone to non-specific enrichment in ChIP and give rise to ‘Phantom Peaks’. These peaks are not obtained with pre-immune serum and are not prominent in input chromatin. Examination of various ACF1 and RSF1 antibodies in Drosophila melanogaster embryos which are wildtype or mutant for the antibody targets.

2015-07-10 | E-GEOD-67323 | biostudies-arrayexpress

Mastitis challenge, Escherichia coli

Project description:Whole transcriptome analysis of milk derived bovine mammary epithelial cells after Escherichia coli challenge

| PRJEB62185 | ENA

DNase Hypersensitivity Peaks from Rat Schwann Cells

Project description:We utilized DNase-Seq to identify open chromatin regions within Schwann cells. This data was used in conjunction with sequence conservation and transcription factor binding site prediction to identify putative cis-regulatory elements critical for Schwann cells. We used three independent biological replicates, and for our studies used sample 'barcode4' as a representative sample for all three. DNase HSS peaks were identified using F-Seq and HOMER, and overlapped to prioritize candidate regions. These regions were then verified using luciferase assays.

2017-08-24 | GSE81669 | GEO

Macrophage Ad5f35 M2 Challenge

Project description:Macrophage Ad5f35 M2 Challenge

| PRJNA491519 | ENA