Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Benchmark of chromatin-protein interaction methods in haploid round spermatids

ABSTRACT: Benchmark of chromatin-protein interaction methods in haploid round spermatids

PROVIDER: PRJNA1209986 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR31984620_1.fastq.gz	Fastqsanger.gz
	SRR31984620_2.fastq.gz	Fastqsanger.gz
	SRR31984621_1.fastq.gz	Fastqsanger.gz
	SRR31984621_2.fastq.gz	Fastqsanger.gz
	SRR31984622_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

Benchmark of chromatin-protein interaction methods in haploid round spermatids

Project description:Chromatin-protein interactions are fundamental for the regulation of gene transcription. While ChIP-seq has long been the standard method for mapping these interactions, emerging techniques such as CUT&RUN and CUT&Tag, which offer advantages including low input requirements and high signal-to-noise ratios, have garnered attention. However, these enzyme-based tagmentation approaches may introduce potential biases, and comparative assessment with ChIP-seq remain absent. This study aims to systematically evaluate and compare the performance of ChIP-seq, CUT&Tag, and CUT&RUN for profiling genome-wide transcription factors and histone modifications binding. This study provides a comprehensive evaluation of ChIP-seq, CUT&Tag, and CUT&RUN for detecting active and repressive histone modifications as well as transcription factor binding. Our results show that all three methods reliably detect histone modifications and transcription factor enrichment, with CUT&Tag demonstrating a relatively higher signal-to-noise ratio. Rigorous peak comparison analysis identified differential enrichment sites detected by the three methods. Additionally, we observed a notable correlation between CUT&Tag signal intensity and chromatin accessibility, suggesting the potential for CUT&Tag to detect regions of active chromatin.

2025-05-13 | GSE286751 | GEO

Expression data from E12.5 male fatal PGCs, PGCLC in vitro, round spermatids and spermatids like cells produced in vitro

Project description:Generation of haploid gametes in vitro can potentially address gamete failure-based infertility.This study reports complete in vitro meiosis from murine ESC-derived PGCLCs resulting in the formation of male spermatid-like cells (SLCs) capable of producing viable fertile offspring via intracytoplasmic sperm injection (ICSI).Our findings provide the basis for generation of haploid spermatids in vitro in human, the generation of transgenic animals, and the use of this system to investigate mechanisms of meiosis. We used microarrays to compare gene expression profiles of in vivo and in vitro derived PGC cells and round spermatids. We collected E12.5 male fatal PGCs, PGCLC in vitro, round spermatids and spermatids like cells produced in vitro, each sample has 3 replications.

2016-02-26 | E-GEOD-71478 | biostudies-arrayexpress

Round Spermatids and Pachytene Spermatocytes

Project description:Mouse Round Spermatids (Sptd) and Pachytene Spermatocytes (Spcy) Keywords: repeat sample

2005-03-15 | GSE1768 | GEO

Round Spermatids and Pachytene Spermatocytes

Project description:Mouse Round Spermatids (Sptd) and Pachytene Spermatocytes (Spcy)

2010-06-10 | E-GEOD-1768 | biostudies-arrayexpress

Expression data from purified control and BrdtΔBD1 round spermatids.

Project description:Brdt is a testis specific member of a family of chromatin interacting proteins. All of the family members have been shown to regulate transcription. Brdt is highly expressed in round spermatids, and may play a role in transcriptional regulation in these cells. We investigated transcriptional changes in mutant round spermatids that were homozygous for a mutation in which the first bromodomain of Brdt was removed. Round spermatids were purified from seven adult animals of each genotype for each Affymetrix microarray. Purity of round spermatids was assessed by propidium iodide staining.

2011-10-20 | E-GEOD-33132 | biostudies-arrayexpress

Expression data from purified control and BrdtΔBD1 round spermatids.

2011-10-21 | GSE33132 | GEO

Effect of aging on gene expression in round spermatids from Brown Norway rats

Project description:To investigate the gene expression changes observed with aging in round spermatids from Brown Norway rats. We then performed gene expression analysis using data obtained from RNA-seq of round spermatids at two time points.

2023-01-11 | GSE219040 | GEO

Histone methylation regulates gene expression in the round spermatids to set the RNA payloads of sperm

Project description:Gene expression during spermatogenesis undergoes significant changes due to a demanding sequence of mitosis, meiosis and differentiation. Round spermatids have to prepare for DNA condensation as well as synthesize transcripts of genes required for the differentiation process. However, the mechanisms of gene activation and silencing in round spermatids remain largely unknown. We employed ChIP-seq to figure out the correlation of H3K4me3 and H3K9me3 marks with transcriptional activation and silencing in round spermatids. Out of about 2800 genes identified by H3K4me3 chipseq, transcriptome sequencing in purified round spermatids showed the presence of transcripts corresponding to about 64% of the genes. On the other hand, only about 25% of H3K9me3 enriched genes showed transcription in round spermatids, that too at very low levels. In conclusion, H3K4me3 enrichment in round spermatids correlates significantly with gene expression and H3K9me3 correlates with gene silencing, both of which are equally important for successful spermatogenesis.

2020-06-03 | GSE151608 | GEO

Evaluation of NSUN7 amount in spermatozoa, round and elongated spermatids of mice

Project description:Here we performed target proteomics of NSUN7 on sorted elongated and round spermatids, as well as mature spermatozoa. We showed that NSUN7 is present at all stages of spermiogenesis and is most abundant in round spermatids, which corresponds to the formation of flagellum and fibrous sheath assembly.

2026-01-12 | PXD069148 | Pride

Identification of substrates of ZDHHC19 in mouse haploid spermatids using Acyl RAC

Project description:Reversible palmitoylation is catalyzed by palmitoyltransferase(PAT) from the zinc-finger DHHC domain-containing protein (ZDHHC) family. The Zdhhc19 knockout male mice showed infertility and Zdhhc19 deficient sperm showed severe morphological defects. To identify the candidate substrates of ZDHHC19 in haploid spermatids, we carried out label free mass spectrometry (MS) combined with resin-assisted capture (RAC) methods. This study reveals the role of palmitoylation mediated by ZDHHC19 during spermiogenesis.

2025-09-10 | PXD057735 | Pride

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