Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: GBS of Urochloa humidicola mapping population

PROVIDER: PRJNA703438 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13757167.fastq.gz	Fastqsanger.gz
	SRR13757168.fastq.gz	Fastqsanger.gz
	SRR13757169.fastq.gz	Fastqsanger.gz
	SRR13757170.fastq.gz	Fastqsanger.gz
	SRR13757171.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Urochloa humidicola

Project description:Urochloa humidicola overview

| PRJNA320655 | ENA

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

Urochloa humidicola

Project description:Urochloa humidicola leaves RNA-seq

| PRJNA299275 | ENA

Urochloa humidicola

Project description:Urochloa humidicola Raw sequence reads

| PRJNA509199 | ENA

Lignin production associated genes in Urochloa humidicola

Project description:Lignin production associated genes in Urochloa humidicola

| PRJNA732926 | ENA

Project description:Urochloa ruziziensis families GBS

| PRJNA973612 | ENA