Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HyDrop v2: Scalable atlas construction for training sequence-to-function models

ABSTRACT: HyDrop v2: Scalable atlas construction for training sequence-to-function models

PROVIDER: PRJNA1245282 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR32948900_1.fastq.gz	Fastqsanger.gz
	SRR32948900_2.fastq.gz	Fastqsanger.gz
	SRR32949000_1.fastq.gz	Fastqsanger.gz
	SRR32949000_2.fastq.gz	Fastqsanger.gz
	SRR32948901_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 468

Similar Datasets

HyDrop v2: Scalable atlas construction for training sequence-to-function models

Project description:Deciphering cis-regulatory logic underlying cell type identity is a fundamental question in biology. Single-cell chromatin accessibility (scATAC-seq) data has enabled training of sequence-to-function deep learning models allowing decoding of enhancer logic and design of synthetic enhancers. Training such models requires large amounts of high-quality training data across species, organs, development, aging, and disease. To facilitate the cost-effective generation of large scATAC-seq atlases for model training, we developed a new version of the open-source microfluidic system HyDrop with increased sensitivity and scale: HyDrop v2. We generated HyDrop-v2 atlases for the mouse cortex and Drosophila embryo development and compared them to atlases generated on commercial platforms. HyDrop-v2 data integrates seamlessly with commercially available chromatin accessibility methods (10x Genomics). Differentially accessible regions and motif enrichment across cell types are equivalent between HyDrop-v2 and 10x atlases. Sequence-to-function models trained on either atlas are comparable as well in terms of enhancer predictions, sequence explainability, and transcription factor footprinting. By offering accessible data generation, enhancer models trained on HyDrop-v2 and mixed atlases can contribute to unraveling cell-type specific regulatory elements in health and disease.

2025-04-02 | GSE293575 | GEO

Construction the adult earthworm cell atlas at single cell resolution.

Project description:Construction the adult earthworm cell atlas at single cell resolution.

| PRJNA752294 | ENA

Construction the adult Drosophila cell atlas at single cell resolution

Project description:Construction the adult Drosophila cell atlas at single cell resolution

| PRJNA737473 | ENA

Construction and Application of an Epigenetic Atlas of the Human Heart

Project description:Construction and Application of an Epigenetic Atlas of the Human Heart

| PRJNA610039 | ENA

Construction the larval and adult zebrafish cell atlas at single cell resolution

Project description:Construction the larval and adult zebrafish cell atlas at single cell resolution

| PRJNA737474 | ENA

Streptomyces sp. V2 strain:V2

Project description:Streptomyces sp. V2 strain:V2 Genome sequencing and assembly

| PRJNA464385 | ENA

Acinetobacter sp. V2 strain:V2

Project description:Acinetobacter sp. V2 strain:V2 Genome sequencing and assembly

| PRJNA275383 | ENA

Construction of Reusable Plasmid Libraries for Strain Construction

Project description:Construction of Reusable Plasmid Libraries for Strain Construction

| PRJNA189258 | ENA

Construction the adult Drosophila cell atlas at single cell resolution

Project description:Single-cell mRNA sequencing (mRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio) and fruit fly (Drosophila melanogaster) are still lacking. Here, we construct the zebrafish and Drosophila cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila, and studying difference between vertebrates and Invertebrates at single cell level.

2022-07-08 | GSE178149 | GEO

Construction the adult earthworm cell atlas at single cell resolution.

Project description:Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio), fruit fly (Drosophila melanogaster) and earthworm (Eisenia andrei) are still lacking. Here, we construct the zebrafish, Drosophila and earthworm cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish, Drosophila and earthworm, and studying difference between vertebrates and Invertebrates at single cell level.

2022-07-08 | GSE181511 | GEO

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