Ontology highlight
ABSTRACT:
PROVIDER: PRJNA664261 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Low temperature is one of the major abiotic stresses limiting rice growth and productivity, it is urgent to reveal the genetic and molecular mechanisms of plant responses to low temperature stress and to search for useful genetic resources for improving low-temperature tolerance. the 8 accessions from China Core Collection include 4 cold tolerance accessions, 3 sensitivity accessions and 1 intermediate type accession. We used microarrays to detail variation of the gene expression after cold treatment and screen more cold-response genes in rice.
2015-10-01 | GSE71680 | GEO
Project description:To understand expression of candidate gene located on QTLs for phosphate sensitivity traits under low P using NtPT1-transgenic rice with increased Pi uptake efficiency and gene expression profile at the V3-stage seedling through the 60K Rice Whole Genome Microarray
2011-04-20 | GSE21377 | GEO
Project description:Evaluation of modulation of the innate immune response during H1N1 infection. The modulatory effect of Single-stranded oligonucleotides (ssON) on monocyte-derived dendritic cells (MoDCs) are evaluated. RNAseq data are used to study the effect on the transcriptome of MoDCs, during infection with simultaneous addition of ssON. Further mechanistic information are added via RNAseq data on poly I:C stimulated MoDCs (Toll-Like Receptor 3 agonist). Control samples are included to perform differential expression analysis. Provided are the fastq files, obtained in the following manner: The RNA sequencing was performed with the TruSeq RiboZero kit from Illumina, 25 M reads per sample and 2x125bp. Read quality were assessed using FastQC (Version 0.11.5) Trim Galore (Version 0.3.6) was used for adapter removal and quality trimming with a quality threshold of 20 on the Phred scale. Count files was created out of the trimmed fastq by mapping high-quality reads to Homo sapiens UCSC hg38 (GRCh38.77) reference genome using STAR aligner (version 2.5) with default values and the parameter out Reads Unmapped set to Fastx in order to extract the unmapped reads. After STAR alignment, the count data for the aligned reads were generated with HTSeq-count (version 0.6.1). The-m parameter was set to union.
2019-05-03 | E-MTAB-7803 | biostudies-arrayexpress
Project description:Whole genome transcriptional responses is profiled in the 0 & 120 mM NaCl stressed whole seedlings of four indica (Pokkali, PSBRc50, IR 58, BRRI dhan 29), two Japonica (Banikat, Nipponbare) and two wild (O. latifolia, O. Rufipogon) accessions of rice (that showed varied level of tolerance to salt stresses) to identify the salinity induced transcripts. Stress was imposed on 14 day old seedlings and total RNA from the whole seedlings was collected after 48 h of stressed period (i.e., from 16 day old seedlings). These data sets were used for two different analyses. Firstly, the gene expression responses of eight rice genotypes was interrogated by the weighted continuous morpho-physiological trait responses (on a scale of 0 to 1) using a modified version of the ‘Significance Analysis of Microarrays’ (SAM) to identify the genes whose expression changes significantly and which is relative to the changes in morpho-physiological traits over these rice genotypes. Secondly, the differentially expressed significant salinity induced genes were also identified in the tolerant and in the susceptible genotypes using Gene-spring software. The genes that enriched the important biological processes and molecular functions (as identified by Gene Ontology: Singular enrichment analysis) are discussed in a way to explain the roles of these genes in overall stress adaptation mechanism.
2016-03-10 | GSE79043 | GEO
Project description:Twelve chili pepper accessions, six domesticated, four wild and two F1 crosses were studied. RNA-Seq experiments were performed with fruits from each accession at 7 different times after anthesis. Additionally, samples of seedlings from two accessions were evaluated. The data set is comprised by 179 samples, that in total have more than 3 billion reads map to the Capsicum annuum genome.
2021-03-16 | GSE165448 | GEO
Project description:Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic modifier Smchd1 in mouse lymphoma cell lines. Methods: Total RNA was extracted using QIAGEN RNeasy Minikit from sorted lymphoma cell lines derived from mice either wild-type or null for Smchd1. 1µg total RNA was used to generate sequencing libraries for whole transcriptome analysis with Illumina’s TruSeq RNA Sample Preparation Kit v2 as per standard protocols. Libraries were sequenced on HiSeq 2000 with Illumina TruSeq SBS Kit v3-HS reagents as either 100 bp single-end or paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.10.5) (Liao et al. 2013). Mapped reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014).
2015-03-13 | GSE64099 | GEO
Project description:Whole genome transcriptional responses is profiled in the 0 & 120 mM NaCl stressed whole seedlings of four indica (Pokkali, PSBRc50, IR 58, BRRI dhan 29), two Japonica (Banikat, Nipponbare) and two wild (O. latifolia, O. Rufipogon) accessions of rice (that showed varied level of tolerance to salt stresses) to identify the salinity induced transcripts. Stress was imposed on 14 day old seedlings and total RNA from the whole seedlings was collected after 48 h of stressed period (i.e., from 16 day old seedlings). These data sets were used for two different analyses. Firstly, the gene expression responses of eight rice genotypes was interrogated by the weighted continuous morpho-physiological trait responses (on a scale of 0 to 1) using a modified version of the â??Significance Analysis of Microarraysâ?? (SAM) to identify the genes whose expression changes significantly and which is relative to the changes in morpho-physiological traits over these rice genotypes. Secondly, the differentially expressed significant salinity induced genes were also identified in the tolerant and in the susceptible genotypes using Gene-spring software. The genes that enriched the important biological processes and molecular functions (as identified by Gene Ontology: Singular enrichment analysis) are discussed in a way to explain the roles of these genes in overall stress adaptation mechanism. Fourteen day old whole seedlings of 8 rice genotypes were treated with 0 & 120 mM NaCl stress for 48 hours each with three replications and the gene expressions were measured using Agilent Rice Gene Expression 4x44K Microarray.
2016-03-10 | E-GEOD-79043 | biostudies-arrayexpress
Project description:Purpose: The aim of this study is to determine the relative expresson levels of mRNA transcripts in wild type platelets Methods: Total RNA was extracted and purified from purified platelets from BALB/c male mice (3 independent samples). Platelet purification was performed as described in Josefsson EC et al, Journal of Experimental Medicine (2011) 208:2017-31. Total RNA (100 ng) was used to generate sequencing libraries for whole transcriptome analysis following Illumina’s TruSeq RNA v2 sample preparation protocol. Completed libraries were sequenced on HiSeq 2000 with TruSeq SBS Kit v3- HS reagents (Illumina) as 100 bp paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and counts for known genes were obtained using the Rsubread package (version 1.18.0) (Liao et al. 2013; Liao et al. 2014).
2016-04-16 | GSE75896 | GEO
Project description:Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain Methods: Total RNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) from cultured neural stem cells derived from male mouse E14.5 brains either wild-type or null for Smchd1. 1 µg total RNA was used to generate sequencing libraries for whole transcriptome analysis with Illumina’s TruSeq RNA Sample Preparation Kit v2 as per standard protocols. Libraries were sequenced on HiSeq 2000 with Illumina TruSeq SBS Kit v3-HS reagents as either 100 bp single-end or paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.10.5) (Liao et al. 2013). Mapped reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014).
2015-06-11 | GSE65747 | GEO