Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of roots of Schrenkiella parvula seedlings treated with 0mM or 175mM NaCl for 0 h, 3 h, 24 h and 48 h.

ABSTRACT: The purpose of the experiments is to understand transcriptional reprogramming in roots of halophyte Schrenkiella parvula (S. parvula) that may contribute to its high salt tolerance. Root materials were harvested from S. parvula seedlings grown on agar plates with ½ strength Murashige-Skoog (½MS) medium including vitamins for 4 days and transferred to ½MS medium supplemented with 0mM or 175mM NaCl for 0h, 3h, 24h or 48h.

INSTRUMENT(S): Illumina NovaSeq 6000

SUBMITTER: Hongfei Li

PROVIDER: E-MTAB-12424 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Samples used in the study originated from three UK sites: the Walton Centre for Neurology and Neurosurgery in Liverpool, the Salford Royal Hospital in Salford and the Southern General Hospital in Glasgow. We recruited patients with pharmacoresistant mesial temporal lobe epilepsy for whom a therapeutic temporal lobectomy was being undertaken. After surgery, the hippocampus was divided into two portions: (1) one portion was preserved for RNA isolation, and (2) the other portion underwent histological analysis by an experienced neuropathologist. Frozen post-mortem histologically-normal hippocampal samples from donors with no known brain diseases were obtained from the MRC Edinburgh Brain Bank (Edinburgh, UK) and the Queen Square Brain Bank (London, UK). Brain samples were disrupted and homogenized in an appropriate volume of QIAzol lysis reagent (Qiagen, Crawley, United Kingdom) by using a TissueRuptor handheld rotor-stator homogenizer (Qiagen, Crawley, United Kingdom). Total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Mini Kit (Qiagen, Crawley, United Kingdom), according to the manufacturer’s instructions. RNA quality was examined by capillary electrophoresis on an Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA) and Agilent 2100 Expert software was used to calculate the RNA Integrity number (RIN) of each sample. Purity of the RNA sample was assessed using a NanoDrop1000 Spectrophotometer. Capillary electrophoresis traces were also examined. Samples with RNA integrity number scores (RIN) below 6, obvious RNA degradation, significant 18S or 28S ribosomal RNA degradation, ratio of absorbance at 260nm and 280nm <1.95, or with noticeable DNA or background contaminants did not pass QC, and were withheld from microarray analysis. The microarrays were processed at the Centre for Genomics Research in the University of Liverpool (http://www.liv.ac.uk/genomic-research/). 50ng of total RNA was amplified and labelled using the Agilent Low Input Quick Amp One-Colour Labeling Kit and labelled RNA was hybridized to Agilent SurePrint G3 Custom Exon 8x60K Microarrays designed to contain probes for each exon of 936 selected genes, including all known SLC genes. Standard Agilent protocols were followed. One array failed on five of the QC criteria and, hence, was excluded. Intensity data were extracted from the remaining arrays using the Feature Extraction Software, in line with the manufacturer’s recommendations. The uploaded files contain data both for a custom exon array designed to contain probes for each exon of 936 selected genes and for a custom gene expression array designed to contain gene expression probes for genes across the whole genome.

Dataset Information

RNA-seq of roots of Schrenkiella parvula seedlings treated with 0mM or 175mM NaCl for 0 h, 3 h, 24 h and 48 h.

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