Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integration of ATAC-seq and RNA-seq identifies key genes in light induced primordium formation of Sparassis latifolia

ABSTRACT: Integration of ATAC-seq and RNA-seq identifies key genes in light induced primordium formation of Sparassis latifolia

PROVIDER: PRJNA533333 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8924630_1.fastq.gz	Fastqsanger.gz
	SRR8924630_2.fastq.gz	Fastqsanger.gz
	SRR8924621_1.fastq.gz	Fastqsanger.gz
	SRR8924621_2.fastq.gz	Fastqsanger.gz
	SRR8924631_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Integration of ATAC-seq and RNA-seq identifies key genes in light induced primordium formation of Sparassis latifolia

Project description:Differential expression profiling of light induction and primordium differentiation was established by integrating ATAC-seq (assay for transposase accessible chromatin with high through put sequencing) and RNA-seq technology. Key genes in light induced the primordium formation of S. latifolia were identified by bioinformatics methods.

2020-02-05 | GSE129983 | GEO

Transcriptome analysis of pine wood decaying mechanism of Sparassis latifolia

Project description:To explore the pine wood decaying mechanism of Sparassis latifolia, we use RNA-seq to detect the gene expression.

2022-11-23 | GSE173822 | GEO

Sparassis latifolia

Project description:Sparassis latifolia overview

| PRJNA316887 | ENA

Long non-coding RNAs and their potential function in postharvest senescence of Sparassis latifolia packaged with oriented polypropylene film

Project description:To investigate the role of lncRNAs in postharvest senescence of Sparassis latifolia, We stored the fruiting bodies of S. latifolia at 4 ℃ for 0, 8, 16 and 24 days with OPP film packaging after harvest and profiled the lncRNA and mRNA transcriptome. We then performed gene expression profiling analysis using data obtained from RNA-seq of fruiting body at 4 time points.

2024-01-17 | GSE226806 | GEO

Sparassis latifolia

Project description:Raw sequence reads of Sparassis latifolia genome

| PRJNA319285 | ENA

Sparassis latifolia strain:CCMJ1100

Project description:Sparassis latifolia CCMJ1100 Standard Draft genome sequencing

| PRJNA347223 | ENA

Sparassis latifolia strain:CCMJ1100 | isolate:CCMJ1100

Project description:Sparassis latifolia CCMJ1100 Transcriptome - YBCB713-M

| PRJNA403237 | ENA

Integration of ATAC-Seq and RNA-Seq Identifies Key Genes in Light-Induced Primordia Formation of Sparassis latifolia.

Project description:Light is an essential environmental factor for Sparassis latifolia primordia formation, but the molecular mechanism is still unclear. In this study, differential expression profiling of light-induced primordia formation (LIPF) was established by integrating the assay for transposase accessible chromatin by sequencing (ATAC-seq) and RNA-seq technology. The integrated results from the ATAC-seq and RNA-seq showed 13 down-regulated genes and 17 up-regulated genes in both the L vs. D and P vs. D groups, for both methods. According to the gene ontology (GO) annotation of these differentially expressed genes (DEGs), the top three biological process categories were cysteine biosynthetic process via cystathionine, vitamin B6 catabolic, and glycine metabolic; the top three molecular function categories were 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, glycine binding, and pyridoxal phosphate binding; cellular component categories were significantly enriched in the glycine cleavage complex. The KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed that these genes were associated with vitamin B6 metabolism; selenocompound metabolism; cysteine and methionine metabolism; glycine, serine, and threonine metabolism; and glyoxylate and dicarboxylate metabolism pathways. The expression of most of the DEGs was validated by qRT-PCR. To the best of our knowledge, this study is the first integrative analysis of ATAC-seq and RNA-seq for macro-fungi. These results provided a new perspective on the understanding of key pathways and hub genes in LIPF in S. latifolia. It will be helpful in understanding the primary environmental response, and provides new information to the existing models of primordia formation in edible and medicinal fungi.

| S-EPMC6981827 | biostudies-literature

Sparassis latifolia strain:minxiu NO.1

Project description:Sparassis latifolia strain:minxiu NO.1 Raw sequence reads

| PRJNA316753 | ENA

Sparassis latifolia strain:minxiu NO.1

Project description:Sparassis latifolia strain:minxiu NO.1 Transcriptome or Gene expression

| PRJNA316665 | ENA