Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: T2T - CHM13

PROVIDER: PRJNA686988 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
		Other
	SRR10035390_1.fastq.gz	Fastqsanger.gz
	SRR10035390_2.fastq.gz	Fastqsanger.gz
	SRR10035391_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 111

Similar Datasets

Homo sapiens isolate:CHM13

Project description:T2T - CHM13

| PRJNA559484 | ENA

Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells

Project description:Centromere identity is defined and maintained epigenetically by the presence of the histone variant CENP-A. How centromeric CENP-A position is specified and precisely maintained through DNA replication is not fully understood. The recently released Telomere-to-Telomere (T2T-CHM13) genome assembly containing the first complete human centromere sequences provides a new resource for examining CENP-A position. Mapping CENP-A position in clones of the same cell line to T2T-CHM13 identified highly similar CENP-A position following multiple cell divisions. In contrast, centromeric CENP-A epialleles were evident at several centromeres of different human cell lines, demonstrating the location of CENP-A enrichment and site of kinetochore recruitment varies among human cells. Across the cell cycle, CENP-A molecules deposited in G1 phase are maintained at their precise position through DNA replication. Thus, despite CENP-A dilution during DNA replication, CENP-A is precisely reloaded onto the same sequences within the daughter centromeres, maintaining unique centromere identity among human cells.

2023-01-01 | GSE221541 | GEO

Telomeric Repeat-Containing RNA Increases in Aged Human Cells

Project description:Telomeric repeat-containing RNA (TERRA), transcribed from subtelomeric regions towards telomeric ends, poses challenges in deciphering its complete sequences. Utilizing TERRA-capture RNA-seq and Oxford Nanopore direct RNA sequencing to acquire full-length TERRA, we annotate TERRA transcription regions in the human T2T-CHM13 reference genome. TERRA transcripts encompass hundreds to over a thousand nucleotides of telomeric repeats, predominantly originating from 61-29-37 bp repeat promoters enriched with H3K4me3, RNA pol II, CTCF, and R-loops. We develop a bioinformatics tool, TERRA-QUANT, for quantifying TERRA using RNA-seq datasets and find that TERRA increases with age in blood, brain, and fibroblasts. TERRA upregulation in aged leukocytes is confirmed by RT-qPCR. Single-cell RNA-seq analysis demonstrates TERRA expression across various cell types, with upregulation observed in neurons during human embryonic stem cell differentiation. Additionally, TERRA levels are elevated in brain cells in the early stage of Alzheimer’s disease. Our study provides evidence linking TERRA to human aging and diseases.

2025-06-09 | GSE250303 | GEO

Homo sapiens

Project description:CHM13 ChrX BAC assembly

| PRJNA631298 | ENA

Open Genomes Telomere-to-Telomere (T2T) Reference Realignment Project

Project description:This project realigns reads from publicly available genomes to the new Telomere-to-Telomere (T2T) CHM13-HG002 reference genome.

| PRJEB11561 | ENA

Human Pangenome Reference Consortium Pangenomes Built With Minigraph (CHM13-Based)

Project description:HPRC Pangenomes: Minigraph (CHM13-Based)

| PRJEB55385 | ENA

Human Pangenome Reference Consortium Pangenomes Built With Minigraph-CACTUS (CHM13-Based)

Project description:HPRC Pangenomes: Minigraph-CACTUS (CHM13-Based)

| PRJEB55387 | ENA

Homo sapiens isolate:CHM13

Project description:WGS of CHM13 with PacBio CCS

| PRJNA530776 | ENA

Project description:Salbum T2T genome

| PRJNA1127301 | ENA

A complete telomere-to-telomere genome of bread wheat presents insights into the evolution, transcriptome, and proteome of a hexaploid genome

Project description:The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here, we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. reference genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 ribosomal DNA(rDNA) units. Genome-wide rearrangements, centromeric elements, TE expansion, and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, TE insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence (HC) protein-coding genes. However, in such a hexaploidy genome, 20.05%, 33.43%, and 42.76% of gene transcript levels, alternative splicing events, and protein levels were detected unbalancing among subgenomes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity, and provides insights for future wheat research and breeding.

2024-12-29 | PXD050500 | 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