Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of grxs17 seedlings

ABSTRACT: RNA was isolated from 14 day old Arabidopsis grxs17 seedlings in three biological repeats using the RNeasy Plant Mini Kit (Qiagen) and DNase I treated (Promega). A TruSeq RNA-Seq library (Illumina) was compiled and sequenced as 50-bp single read using Illumina HiSeq 2000. Control samples can be found in submission E-MTAB-3916.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Laurens Pauwels

PROVIDER: E-MTAB-5001 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq analysis of wild type Columbia seedlings

Project description:RNA was isolated from 14 day old Arabidopsis Col-0 seedlings in three biological repeats using the RNeasy Plant Mini Kit (Qiagen) and DNase I treated (Promega). A Trueseq RNA-Seq library (Illumina) was compiled and sequenced as 50-bp single read using Illumina HiSeq 2000.

2017-08-07 | E-MTAB-3916 | biostudies-arrayexpress

RNAseq analysis of wild type dark grown PSB-D cell cultures

Project description:RNA was isolated from wild-type dark grown PSB-D cell cultures in three biological repeats using the RNeasy Plant Mini Kit (Qiagen) and DNase I treated (Promega). A Trueseq RNA-Seq library (Illumina) was compiled and sequenced as 50-bp single read using Illumina HiSeq 2000.

2017-08-07 | E-MTAB-3915 | biostudies-arrayexpress

RNA-seq analysis of Arabidopsis thaliana cells treated with RN1 and 2,4-D

Project description:A PSB-D wild type Arabidopsis thaliana cell culture (Arabidopsis Biological Resource Center stock: CCL84840) was grown after subculturing for one week and divided into separate 10 mL samples for 24 h. Samples were then treated with 50 µM RubNeddin1 (RN1, Chembridge ID 6389186), 2,4-D, or an equal volume of DMSO. Total RNA was extracted from each 10 mL cell culture sample, for each of at least 3 biological replicates, RQ1 RNase-free DNase (Promega) was used for the on-column DNase digestion step. A Trueseq RNA-Seq library (Illumina) was compiled and sequenced as 50-bp single read using Illumina HiSeq 2000. Control samples (3) for this experiment were submitted under accession number E-MTAB-3915

2021-08-03 | E-MTAB-7761 | biostudies-arrayexpress

Transcriptome-wide analysis of gene expression in dark-grown WT and pif mutant seedlings

Project description:We sequenced mRNA from WT and PhytochromeInteractingFactor (pif) mutant seedlings grown for 2d in darkness. Transcriptome profiles of the wild-type (WT), pif1, pif3, pif, pif5 monogenic mutants, pif3pif4pif5 (pif345), pif1pif4pif5(pif145), pif1pif3pif5 (pif135) and pif1pif3pif4 (pif134) triple mutants and pif1pif3pif4pif5 (pifq) quadruple mutant seedlings. Biological triplicate samples were analyzed from libraries constructed using a 3'-capture, 5' to 3' directional method.

2014-10-02 | E-GEOD-42665 | biostudies-arrayexpress

Identification of the FRS12 regulated genes by RNA-Seq Analysis in Arabidopsis thaliana

Project description:To identify genes regulated by FRS12 at night time, stratified Arabidopsis thaliana transgenic seedlings expressing Pro35S:FRS12-GR and Pro35S:GFP-GR were grown in 1/2 MS with 1% sucrose liquid medium under long days (16:8) conditions and treated with 5uM of dexametasone 4H before harvesting at night time at zeitgeber time 23 (time of lights on usually defines zeitgeber time zero). Three biological replicates were harvested for each line. RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) and DNase I treated (Promega). RNA samples were processed by first preparing a TruSeq RNA-Seq library (Illumina) and sequenced at 50bp single read using Illumina HiSeq 2000.

2017-02-04 | E-MTAB-3018 | biostudies-arrayexpress

Transcriptome analysis of the newly described centipede Eupolybothrus cavernicolus sp.n.

Project description:We compiled the transcriptome by extracting mRNA, reverse transcription and Illumina sequencing, followed by assembly and annotation by comparison with public databases (including; Nr, SwissProt and COG). Quantitative data on the transcription abundance of each putative protein sequence is provided as assesed by the SOAPdenovo_trans assembly tool.

2013-10-28 | E-MTAB-1859 | biostudies-arrayexpress

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

Transcriptomics of Arabidopsis thaliana nrpd1-3 and nrpd1-3 plant 2L under control or heat stress

Project description:The intent of the experiment was to infer differential heat-induced transncriptional disturbance of genes in a background with novel insertions of ONSEN/Copia78 LTR retrotransposon. For this, we performed Illumina 150 bp pair-end RNA-seq, in RdDM mutant nrpd1-3 and a line with numerous ONSEN neo-insertions (nrpd1-3 plant 2L); under control and heat stress.

2019-03-16 | E-MTAB-5884 | biostudies-arrayexpress

Transcriptomics of Arabidopsis thaliana wild-type and nrpd1-3 under control or heat stress

Project description:The intent of the experiment was to infer from transcriptome data the differential activation of LTR retrotransposon family members from Onsen/COPIA78, an Arabidopsis thaliana's heat-activated retrotransposon. For this, we performed Illumina 150 bp pair-end RNA-seq, in both wild-type Col-0 and RdDM mutant nrpd1-3 under control and heat stress.

2019-03-17 | E-MTAB-5643 | biostudies-arrayexpress

Identification of polyA sites in Drosophila melanogaster

Project description:The 3' ends of most Drosophila melanogaster genes are poorly annotated or are determined by only a single EST or cDNA clone. To enhance the annotation of poly(A) site use in Drosophila, we performed deep sequencing on RNA isolated from 29 dissected tissues using an approach designed to enrich for poly(A) spanning reads. From these experiments, we identified 1.4 million poly(A) spanning reads leading to the identification of many new poly(A) sites and the identification of many tissue-specific poly(A) sites. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf RNA from 29 dissected Drosophila melanogaster tissues (in duplicate) were used to prepare polyA enriched RNA-Seq libraries. Briefly, total RNA was poly(A) selected, fragmented, and ligated to 5' and 3' RNA linkers. These libraries were amplified using Illumina paired-end primers, and subsequently reamplified using a 3' primer complementary to the 3' adapter but containing 6 Ts at the 3' end. The libraries were also multiplexed and up to 12 samples mixed per lane and sequenced on an Illumina GAIIx using paired-end 76 bp reads, or an illumina HiSeq 2000 using paired-end 100 bp reads. All reads were mapped to the Drosophila melanogaster genome to identify unmapped reads. Unmapped reads containing at least 10 A residues at the 3' end were identified, the terminal A residues trimmed, realigned to the genome to identify uniquely mapped reads. Such reads were identified as polyA spanning reads

2011-11-23 | E-GEOD-33905 | 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