Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of four-week-old shoot tissues of wild type (Col-0) and dph1 mutants (in Col-0 background) growing in soil under normal growth conditions

ABSTRACT: This is comparative transcriptomics by using the wild type and dph1 mutants to see the change of dph1 mutants at transcript levels compared with wild type. Rosette tissues of four-week-old plants grown in soil were harvested for total RNA isolation by RNeasy Plant Mini Kit (Qiagen). Libraries were prepared and sequenced using the Illumina platform by Novogene (Hongkong, CN). For RNA-seq data analysis, raw reads were first filtered by CutAdapt 2.1 to remove adaptors and low quality reads. The filtered reads were mapped to Arabidopsis thaliana Col-0 reference genome (Tair 10). Read counts were determined by Qualimap2. Differentially expressed genes were identified using the R package DESeq2.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Hongliang Zhang

PROVIDER: E-MTAB-11206 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of two-week-old seedlings of wild type (Col-0), dph1 and dph2 mutants (in Col-0 background) growing on 0.5x MS media with 0.5% (w/v) sucrose under normal growth conditions (16 h light/8 h dark).

Project description:This is comparative transcriptomics by using the wild type, dph1 and dph2 mutants to see the change of dph1 and dph2 mutants at transcript levels compared with wild type. Seedlings of two-week-old plants grown in liquid MS media were harvested for total RNA isolation by RNeasy Plant Mini Kit (Qiagen). Libraries were prepared and sequenced using the Illumina platform by Novogene (Cambridge, UK). For RNA-seq data analysis, raw reads were first filtered by CutAdapt 2.1 to remove adaptors and low-quality reads. The filtered reads were mapped to Arabidopsis thaliana Col-0 reference genome (Tair 10). Read counts were determined by Qualimap2. Differentially expressed genes were identified using the R package DESeq2.

2024-03-01 | E-MTAB-13779 | biostudies-arrayexpress

Sequencing of siRNA from soybean containing silencing vectors and empty vectors

Project description:A cDNA library was constructed by Novogene (CA, USA) using a Small RNA Sample Pre Kit, and Illumina sequencing was conducted according to company workflow, using 20 million reads. Raw data were filtered for quality as determined by reads with a quality score > 5, reads containing N < 10%, no 5' primer contaminants, and reads with a 3' primer and insert tag. The 3' primer sequence was trimmed and reads with a poly A/T/G/C were removed

2021-07-21 | GSE180131 | GEO

RNA-seq in Arabidopsis thaliana Col and hcr3 mutant

Project description:RNA-prep of Col and hcr3 mutant from seedling or bud sample. RNA was extracted using the RNeasy plant (Qiagen, 74904) and sent to BGI Hongkong for RNA-seq library construction and sequencing. Briefly, mRNA enriched by using oligo dT beads were fragmented and used for cDNA synthesis. dUTP method was used for cDNA synthesis to make the RNA-seq library strand-specific. The constructed library was amplified to make DNA nanoball (DNB) and sequenced on DNBSEQ platform.

2023-03-14 | E-MTAB-12699 | biostudies-arrayexpress

Genome-wide maps of RNA-protein interactions of SRSF3, hnRNPK and CPSF6

Project description:C2C12 cells were UV-irradiated at 400 mJ, and whole cell lysates were harvested from the cells. tRIP was performed as previously described (Masuda et al). Samples were sequenced on the Illumina NovaSeq6000 with 150 bp paired-end read (Macrogen, Japan) or Miseq with 150 bp single-read at the core facility of the Nagoya University. For paired-end read data, only P5 reads were used for analysis. Briefly, after standard HiSeq demultiplexing, reads were adapter-trimmed and reads less than 18 bp were discarded using cutadapt (v1.10). Mapping was first performed against the mouse repetitive elements in RepBase with STAR (v2.5.2b). Repeat-mapped reads were removed, and all others were then mapped against the mouse genome (mm10) with STAR (v 2.5.2b). Multiply mapped reads were filtered out. Duplicates of reads uniquely mapped to the human or mouse genome were removed by Picard (v2.0.1).

2021-07-20 | GSE161602 | GEO

Mapping QTLs for 15 morpho-metric traits in <i>Arabidopsis thaliana</i> using Col-0 × Don-0 population.

Project description:Genome wide quantitative trait loci (QTL) mapping was conducted in Arabidopsis thaliana using F2 mapping population (Col-0 × Don-0) and SNPs markers. A total of five linkage groups were obtained with number of SNPs varying from 45 to 59 per linkage group. The composite interval mapping detected a total of 36 QTLs for 15 traits and the number of QTLs ranged from one (root length, root dry biomass, cauline leaf width, number of internodes and internode distance) to seven (for bolting days). The range of phenotypic variance explained (PVE) and logarithm of the odds ratio of these 36 QTLs was found be 0.19-38.17% and 3.0-6.26 respectively. Further, the epistatic interaction detected one main effect QTL and four epistatic QTLs. Five major QTLs viz. Qbd.nbri.4.3, Qfd.nbri.4.2, Qrdm.nbri.5.1, Qncl.nbri.2.2, Qtd.nbri.4.1 with PVE > 15.0% might be useful for fine mapping to identify genes associated with respective traits, and also for development of specialized population through marker assisted selection. The identification of additive and dominant effect QTLs and desirable alleles of each of above mentioned traits would also be important for future research.

| S-EPMC7196571 | biostudies-literature

Identifying crossover locations in an Arabidopsis thaliana Col x Di-G F2 population using genotyping by sequencing

Project description:Genomic DNA from 239 Col x Di-G F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al; Yelina et al), with the following modifications. DNA was extracted from 3 rosette leaves of 5 week old plants and 150 ng of DNA used as input for each library. DNA shearing was carried out for 20 minutes at 37°C with 0.4U of DNA Shearase (Zymo research). Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). The barcoded adapter sequences were trimmed and bases with quality lower than 19 were filtered using Cutadapt. Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline.

2024-08-19 | E-MTAB-14382 | biostudies-arrayexpress

Artificial Autopolyploidization Modifies the Tricarboxylic Acid Cycle and GABA Shunt in Arabidopsis thaliana Col-0.

Project description:Autopolyploidy is a process whereby the chromosome set is multiplied and it is a common phenomenon in angiosperms. Autopolyploidy is thought to be an important evolutionary force that has led to the formation of new plant species. Despite its relevance, the consequences of autopolyploidy in plant metabolism are poorly understood. This study compares the metabolic profiles of natural diploids and artificial autotetraploids of Arabidopsis thaliana Col-0. Different physiological parameters are compared between diploids and autotetraploids using nuclear magnetic resonance (NMR), elemental analysis (carbon:nitrogen balance) and quantitative real-time PCR (qRT-PCR). The main difference between diploid and autotetraploid A. thaliana Col-0 is observed in the concentration of metabolites related to the tricarboxylic acid cycle (TCA) and ?-amino butyric acid (GABA) shunt, as shown by multivariate statistical analysis of NMR spectra. qRT-PCR shows that genes related to the TCA and GABA shunt are also differentially expressed between diploids and autotetraploids following similar trends as their corresponding metabolites. Solid evidence is presented to demonstrate that autopolyploidy influences core plant metabolic processes.

| S-EPMC4876396 | biostudies-literature

Transcriptomes of subterranean mammals reveal that naked mole rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles

Project description:We performed RNAseq, metabolomics and pathway enrichment analysis on cardiac tissue from naked mole-rats (Heterocephalus glaber) and from seven other members of African mole rat genera, Cape mole-rat (Georychus capensis), Cape dune mole-rat (Bathyergus suillus), Common mole-rat (Cryptomys hottentotus hottentotus), Natal mole-rat (C. h. natalenesis), Mahali mole rat (C. h. mahali), Highveld mole-rat (C. h. pretoriae) and Damaraland mole-rats (Fukomys damarensis) representing differing burrow and soil types, degrees of sociality, lifespan and hypoxia tolerance. In addition, we include the evolutionarily highly divergent hottentot golden mole (Ambysomus hottentotus), an Afrotherian subterranean, solitary mammal, and the C57/BL6 laboratory mouse as a standard mammal control. After RNA sequencing, we removed the reads mapped to rRNAs and get rawdata, then we filtered the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. These are the data uploaded.

2024-02-20 | E-MTAB-13808 | biostudies-arrayexpress

Control (Col-0) for TGNap1 proteomic analysis

Project description:Control (Col-0) related to TGNap1 coimmunoprecipitation analysis

2019-11-08 | PXD011578 | Pride

Total RNA sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0 in Arabidopsis [msh1_graft_leaf_RNA-seq]

Project description:Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the total RNA sequencing.

2020-09-20 | GSE152565 | GEO

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