Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Linum usitatissimum cultivar:Yiya 5

ABSTRACT: Genome assembly for fiber-use flax

PROVIDER: PRJNA725636 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14339745_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 1 of 1

Similar Datasets

Alternative splicing and DNA methylation interact in linseed (Linum usitatissimum L.) response to different drought stresses

Project description:To investigate changes in genome methylation in flax seedlings under drought stress, we selected a drought-tolerant flax variety (Z141) and a drought-sensitive flax variety (NY-17) We then performed genome methylation analysis using data obtained from Z141 and NY-17 leaf tissue BS-seq at four different treatments (DS, RW, RD and CK).

2023-07-14 | GSE213719 | GEO

gene expression analysis in different tissues of Flax (Linum usitatissimum L.)

Project description:We developped a new oligo microarray platform to analyse flax transcriptome. Here, we validated this microarray on several tissues of flax, at different developmental stages.

2010-06-15 | GSE21868 | GEO

Whole-genome DNA methylation landscapes of control and heat-stressed Linum usitatissimum seedlings.

Project description:Whole-genome bisulfite sequencing (WGBS) was employed for identification of differential DNA methylation profiles among control and heat-stressed seedlings of a fibre flax (Linum usitatissimum L.) var., JRF-2. It was identified as a tolerant variety of heat stress-induced oxidative damage. High-quality genomic DNA from four samples comprised 3-week-old control and heat-stressed (40±2°C) seedlings, with or without treated with 5-Azacytidine (hypomethylating agent). High-quality and filtered paired-end Illumina reads were aligned to the flax reference genome, assembled in chromosomes, using bwa-meth tool, followed by methylation loci (5-mC) calling using the MethylDackel software. Differentially methylated regions (DMRs) between the control and other samples were identified using the methylKit and annotated using genomation package for their precedence in the promoter/exon/intron/intergenic regions. The DMRs comprised both hyper- and hypomethylated loci, but the latter found dominated due to heat stress in flax seedlings. The WGBS in flax for heat stress will provide a platform to identify epigenetic loci responsible for heat-stress adaptation in flax.

2022-04-01 | GSE185571 | GEO

Linum usitatissimum

Project description:Transcriptomics modifications in inner stem tissues of the flax lignified bast fiber mutant1 (lbf1)

| PRJNA260724 | ENA

Linum usitatissimum

Project description:Transcriptomics modifications in outer stem tissues of the flax lignified bast fiber mutant1 (lbf1)

| PRJNA260725 | ENA

Expression analysis of Linum usitatissimum 25-mers and 60-mers arrays

2012-05-15 | GSE37980 | GEO

Expression analysis of Linum usitatissimum 25-mers and 60-mers arrays

Project description:Performances of flax gene expression analyses were compared in two categories of Nimblegen microarrays (short 25-mers oligonucleotides and long 60-mers oligonucleotides) Results obtained in this study are described in Intra-platform comparison of flax (Linum usitatissimum L.) high-density Nimblegen DNA microarrays submitted to Journal of Computational Biology We compared two categories of flax target probes: short (25-mers) oligonucleotides and long (60-mers) oligonucleotides in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. This comparison was realized with two different flax samples and each RNA sample was used for the two categories of arrays. Experiments were realized in order to discriminate specific gene expression profiles of two different flax tissues (outer and inner stem tissues).

2012-05-14 | E-GEOD-37980 | biostudies-arrayexpress

gene expression analysis in different tissues of Flax (Linum usitatissimum L.)

Project description:We developped a new oligo microarray platform to analyse flax transcriptome. Here, we validated this microarray on several tissues of flax, at different developmental stages. 30 chips study using total RNA from 9 different tissue samples of Flax (Leaf sample at green capsule stage, stem inner tissue at vegetavie stage, stem outter tissue at vegetative stage, stem inner tissue at green capsule stage, stem outter tissue at green capsule stage, roots, embryos of 10, 20 and 40 days after flowering) for an overall survey of microarry accuracy and total RNA from 6 stem tissue at green capsule stage (3 of the cultivar 'Belinka' and 3 of the cultivar 'Drakkar') for an analysis of biological replicates reproducibility.

2010-06-15 | E-GEOD-21868 | biostudies-arrayexpress

RNASeq Analysis of the Shoot Apex of Flax (Linum usitatissimum) to Detect Phloem Fiber Specification Genes

Project description:We used RNAseq to compare transcript expression patterns in two segments of the vegetative stem of 14d flax plants, from which all visible leaves had been removed. The segments were: (i) the apical region (AR) of the shoot apex, which contained the apical-most 0.5 mm of the stem, including the SAM and its immediate derivatives; and (ii) the basal region (BR), which contained the entire stem except for the apical-most 1 cm, and therefore represented all stem and vascular tissues at later stages of differentiation as compared to the AR. These data will help identify genes that contribute to specification of phloem fiber identity.

2016-04-27 | GSE80718 | GEO

Transcription profiling of flax (Linum usitatissimum) developmental series

Project description:Three 2cm segments were excised from different parts (TOP, MID, BOT) along the vertical axis of a 4 week old (25cm) stem of flax (L. usitatissimum) were compared using a cDNA amplicon array. Each segment represented a different developmental stage, especially in relation to bast fibre differentiation (i.e. TOP= elongation, MID=transition, BOT= thickening). Only the cDNAs that showed the highest differential expression were sequenced.

2007-05-01 | E-MEXP-990 | biostudies-arrayexpress

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