Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lignin production associated genes in Urochloa humidicola

ABSTRACT: Lignin production associated genes in Urochloa humidicola

PROVIDER: PRJNA732926 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14662184_1.fastq.gz	Fastqsanger.gz
	SRR14662184_2.fastq.gz	Fastqsanger.gz
	SRR14662185_1.fastq.gz	Fastqsanger.gz
	SRR14662185_2.fastq.gz	Fastqsanger.gz
	SRR14662186_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Lignin production associated genes in Urochloa humidicola

Project description:This study aims to reveal genes related to lignin production in Urochloa humidicola through RNA-Seq. This species is widely used as forrage for cattle, being some species of Urochloa responsible for 85% of pastures in Brazil. Given this importance, lignin is a molecule directly related to low digestibility in cattle. Eight samples were chosen from previous lignin production and forage quality data; four samples had low lignin production, and four had high lignin production. The second extended leaves were collected for RNA extraction using RNeasy® Plant Mini Kit. The cDNA library preparation was generated according to Illumina TruSeq Stranded mRNA Sample Prep kit protocol, and RNA sequencing was performed using HiSeq 2500 sequencer. Quality control was measured by FastQC software v 0.11.8. As Urochloa humidicola does not have a sequenced genome, a transcriptome assembly was built by two approaches: through Trinity v 2.8.4 (Grabherr et al., 2011), and Stringtie v 2.0.4 software (Pertea et al., 2015), using Urochloa ruziziensis as reference genome. Then, the final transcriptome was assembled using those two de novo assembles by PASA v 2.2 (Haas et al., 2003). Salmon v 0.7.2 software (Patro et al., 2017) was used to quantify the sequenced reads. The DEG was identified using DESeq2 package, and genes functions were annotated through Trinotate software (Bryant et al., 2017). In total, approximately 123 million reads were sequenced. The final assembled transcriptome was formed by 48,695 transcripts. The differential expressed genes analysis revealed 258 significatively genes. Here, we highlighted genes related to flavonoid biosynthetic process, regulation of phenylpropanoid metabolic process, and Myb-like DNA-binding domain.

2021-09-30 | GSE175577 | GEO

Lignin production associated genes in Cenchrus purpueus

Project description:Lignin production associated genes in Cenchrus purpueus

| PRJNA731177 | ENA

Lignin production associated genes in Cenchrus purpueus

Project description:This study aims to reveal genes related to lignin production in Cenchrus purpureus through RNA-Seq. This species is widely used as forrage for cattle, and for the last years, due to its high biomass yield, has been considered as source to lignocellulosic ethanol. Given those two importances, lignin is a molecule related to low digestibility in cattle and recalcitrance in biofuel production. Eight samples were chosen from previous lignin production and forage quality data; four samples had low lignin production, and four had high lignin production. The highest nodes were collected for RNA extraction using TRIzol reagent, following Jordon-Thaden et a;. (2015) protocol. The cDNA library preparation was generated according to Illumina TruSeq Stranded mRNA Sample Prep kit protocol, and RNA sequencing was performed using HiSeq 2500 sequencer. Quality control was measured by FastQC software v 0.11.8. The sequenced reads were aligned to Cenchrus purpureus genome through STAR software v. 2.5.2b (Dobin et al., 2012). After that, the transcriptome was assembled using Stringtie v 2.0.4 software (Pertea et al., 2015). Salmon v 0.7.2 software (Patro et al., 2017) was used to quantify the sequenced reads. The DEG was identified using DESeq2 package, and genes functions were annotated through Trinotate software (Bryant et al., 2017). In total, approximately 130 million reads were sequenced. The final assembled transcriptome was formed by 101,169 transcripts. The differential expressed genes analysis revealed 52 significatively genes. Here, we highlighted genes related to sterol, L-serine and terpene biosynthetic process.

2021-10-01 | GSE174718 | GEO

Urochloa humidicola

Project description:Urochloa humidicola overview

| PRJNA320655 | ENA

Urochloa humidicola

Project description:Urochloa humidicola leaves RNA-seq

| PRJNA299275 | ENA

Urochloa humidicola

Project description:Urochloa humidicola Raw sequence reads

| PRJNA509199 | ENA

lignin degradation genes studies in aquatic environment

Project description:lignin degradation genes studies in aquatic environment Metagenome