Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiple tissue RNA sequencing of two Arabidopsis thaliana MAGIC founder accessions

ABSTRACT: We sequenced messenger RNA isolated from seeding, root, and floral bud tissue for 2 MAGIC founder accessions of Arabidopsis thaliana. The resulting data was used for validation of gene models, and provides a resource to assess tissue-specific expression. Examination of RNA expression across tissues (seedling, root, floral bud) for 2 accessions (Col-0, Can-0).

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Richard Clark

PROVIDER: E-GEOD-30795 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.

Gan Xiangchao X Stegle Oliver O Behr Jonas J Steffen Joshua G JG Drewe Philipp P Hildebrand Katie L KL Lyngsoe Rune R Schultheiss Sebastian J SJ Osborne Edward J EJ Sreedharan Vipin T VT Kahles André A Bohnert Regina R Jean Géraldine G Derwent Paul P Kersey Paul P Belfield Eric J EJ Harberd Nicholas P NP Kemen Eric E Toomajian Christopher C Kover Paula X PX Clark Richard M RM Rätsch Gunnar G Mott Richard R

Nature 20110828 7365

Genetic differences between Arabidopsis thaliana accessions underlie the plant's extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accessio ...[more]

PMID: 21874022

Similar Datasets

Multiple tissue RNA sequencing of 17 Arabidopsis thaliana MAGIC founder accessions

Project description:We produced RNA-Seq reads from messenger RNA isolated from seedling, root, and floral bud tissue for 17 MAGIC founder accessions (inbred strains) of Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provide a resource to assess tissue-specific expression across different accessions of A. thaliana. Note that comparable read data for accessions Col-0 and Can-0, which are also founders of the MAGIC lines, has previously been released under GEO series GSE30795 (Gan et al. 2011. Nature, 477:419-23). Examination of RNA expression across tissues (seedling, root, floral bud) for 17 Arabidopsis thaliana accessions (Bur-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, Zu-0).

2013-12-11 | E-GEOD-53197 | biostudies-arrayexpress

Multiple tissue RNA sequencing of two Arabidopsis thaliana MAGIC founder accessions

Project description:We sequenced messenger RNA isolated from seeding, root, and floral bud tissue for 2 MAGIC founder accessions of Arabidopsis thaliana. The resulting data was used for validation of gene models, and provides a resource to assess tissue-specific expression.

2011-08-29 | GSE30795 | GEO

Multiple tissue RNA sequencing of 17 Arabidopsis thaliana MAGIC founder accessions

2013-12-11 | GSE53197 | GEO

Transcriptome sequencing of Prunus mume for different tissues.

Project description:We have sequenced a wild Prunus mume and constructed a reference sequence for this genome. In order to improve quality of gene models, RNA samples of five tissues (bud, leaf, root, stem, fruit) were extracted from the Prunus mume. To investigate tissue specific expression using the reference genome assembly and annotated genes, we extracted RNA samples of different tissues and conducted transcriptome sequencing and DEG analysis. Five RNA pools were created corresponding to different tissues of the Prunus mume.

2012-12-27 | E-GEOD-40162 | biostudies-arrayexpress

H3K4me3-ChIP-seq in Arabidopsis thaliana Col and hcr2 mutant

Project description:Col and hcr2 mutant from seedling and bud sample were harvested. Nuclei extracted using Honda buffer. Cross-linked chromatin was fragmented with mirococcal nuclease (MNase, NEB M0247S). After fragmentation, fragmented chromatin was incubated with H3K4me3 antibody (AbCam ab8580). TruSeq Prep Kit v2 (Illumina) were used for library construction.

2022-03-23 | E-MTAB-10656 | biostudies-arrayexpress

Analysis of pummelo proteome using iTRAQ

Project description:For protein identification, the following parameters were used. Peptide mass tolerance = 20 ppm, Missed cleavage = 2, MS/MS tolerance = 0.1 Da, Enzyme = Trypsin, Fixed modification: Carbamidomethyl (C), iTRAQ8plex(K), iTRAQ8plex(N-term), Variable modification：Oxidation(M)，Decoy database pattern=Reverse. The MASCOT search results for each SCX elution were further processed using the ProteomicsTools (version 3.1.6) which includes the programs BuildSummary, Isobaric Labeling Multiple File Distiller and Identified Protein iTRAQ Statistic Builder (Information can be accessed from Research Center for Proteome Analysis (http://www.proteomics.ac.cn/).

2020-01-27 | PXD000527 | Pride

ATAC-seq in Arabidopsis thaliana Col and hcr2 mutant

Project description:ATAC-seq of Col and hcr2 mutant from seedling and bud sample. Tagmentation was performed using the Tag DNA enzyme & buffer kit (Illumina, 20034210). Nextera DNA CD Index primers were used for library construction. The indexed libraries were subjected to paired-end 50-bp sequencing using an Illumina HiSeqX instrument (Microgen, Korea).

2022-03-23 | E-MTAB-10790 | biostudies-arrayexpress

RNA-seq in Arabidopsis thaliana Col and hcr2 mutant

Project description:RNA-prep of Col and hcr2 mutant from seedling and bud sample. RNA extracted by Trizol and cDNA was synthesized by using the ScriptSeq v2 RNA-seq Library Preparation Kit (SSV21124, Epicentre). ScriptSeq Index PCR Primers (RSBC10948, Epicentre) were used for library construction.

2022-03-23 | E-MTAB-10791 | biostudies-arrayexpress

Bisulfite-seq in Arabidopsis thaliana Col and hcr2 mutant

Project description:DNA-prep of Col and hcr2 mutant from seedling and bud sample. DNA was extracted using DNeasy Plant Mini Kit (Qiagen 69104, USA). Library construction and bisulfite conversion was performed using EZ DNA Methylation-Gold kit (ZYMO). DNA libraries are sequenced on the DNBseq platform (BGI, Hong Cong).

2022-03-23 | E-MTAB-10657 | biostudies-arrayexpress

Comprehensive analysis of genic male sterility-related genes in Brassica rapa using Brassica rapa 300k microarray v2.0

Project description:To identify genes associated with genic male sterility (GMS) that could be useful for hybrid breeding in Chinese cabbage (Brassica rapa ssp. pekinensis), floral bud transcriptome analysis was carried out using a B. rapa microarray with 300,000 probes (Br300K). Among 47,548 clones deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region, a total of 10,622 genes were differentially expressed between fertile and sterile floral buds; 4,774 and 5,848 genes were up-regulated over 2-fold in fertile and sterile buds, respectively. However, the expression of 1,413 and 199 genes showed fertile and sterile bud-specific features, respectively. Genes expressed specifically in fertile buds, possibly GMS-related genes, included homologs of several Arabidopsis male sterility-related genes, genes associated with the cell wall and synthesis of its surface proteins, pollen wall and coat components, signaling components, and nutrient supplies. However, most early genes for pollen development, genes for primexine and callose formation, and genes for pollen maturation and anther dehiscence showed no difference in expression between fertile and sterile buds. Some of the known genes associated with Arabidopsis pollen development showed similar expression patterns to those seen in this study, while others did not. BrbHLH89 and BrMYP99 are putative GMS genes. Additionally, 17 novel genes identified only in B. rapa were specifically and highly expressed only in fertile buds, implying the possible involvement in male fertility. All data suggest that Chinese cabbage GMS might be controlled by genes acting in post-meiotic tapetal development that are different from those known to be associated with Arabidopsis male sterility. A total of 14 chips were used for the microarray experiment. Experiments were performed with two biological replicates.

2013-10-22 | E-GEOD-47665 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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