biostudies-arrayexpressSandeep SharmaArachis hypogaeahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13805The experiment was conducted to analyze transcriptional and methylome-induced changes in peanuts under salinity stress. We performed RNA sequencing and whole genome bisulfite sequencing (WGBS) of peanut roots after exposure to 150mM of Nacl for 7 days. A large change in expression was observed in various stress-induced pathways, including the RdDM pathway. ALso, the methylation profile showed an association with the expression of genes involved in stress tolerance.biostudies-arrayexpressSequencing - These libraries were sequenced with NextSeq 500 to generate 150 bp end paired end reads on Illumina platformSample Collection - Roots of 4-5 peanut seedlings were pooled and considered as one biological replicateGrowth Protocol - , peanut cv. GG 20 seeds were surface sterilized with 2% sodium hypochlorite and rinsed 4-5 times with sterilized double-distilled water. Seeds were placed in sterile cotton (soaked in ½ MS medium) in a tissue culture bottle and kept in the dark for two days before transfer to a growth chamber. The growth conditions were set at 26 °C and 16h/ 8h light/dark cycle (350 µmol m-2 s-1 light intensity) and seedlings were allowed to grow for 7 days.Nucleic Acid Extraction - Genomic DNA was isolated from the root samples using CTAB method, followed by RNAse A treatment.50-100 ng of purified genomic DNA were treated with Zymo CT conversion reagent in a thermal cycler with defined parameters. The bisulphite treated DNA was purified and used to prepare sequencing library using True Seq Methylation kit (Illumina, Inc. USA).Library Construction - , bisulphite-treated single stranded DNA was random primed using a polymerase that can read Uracil. The 3’ end of newly synthesized DNA strands were tagged with a second specific sequence followed by addition of Illumina adapters at both the DNA strands. The libraries were quantified with Qubit 3.0 and analyzed in 4200 Tape Station System (Agilent Technologies) using high sensitivity D1000 screen tape as per the manufacturer’s instruction.Sample Treatment - Two-weeks old peanut seedlings were subjected to 150 mM NaCl (final concentration in hydroponics growth medium) and root samples were collected after one week of salt treatment.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesSequence Alignment - The clean reads were aligned to the reference peanut genome (https://data.legumeinfo.org/Arachis/hypogaea /genomes/Tifrunner.gnm1.KYV3/) by Bismark Extractor (Version: v0.16.0) with --bowtie2 (-n 2 -l 28 -e 70 parameters ).Data Transformation - Raw sequences were processed to remove unknow nucleotides “N”, adapter sequence and low-quality reads (quality threshold (QV) < 20 phred score and read length <20 nucleotides) (Trimmomatic v0.32). The clean reads were aligned to the reference peanut genome (https://data.legumeinfo.org/Arachis/hypogaea /genomes/Tifrunner.gnm1.KYV3/) by Bismark Extractor (Version: v0.16.0)UnknownTranscriptomicsGenomicsProteomicsNextSeq 500methylation profiling by high throughput sequencingArachis hypogaeaSandeep SharmafalseSalinity-induced transcriptional and DNA methylation reprogramming of peanut roots (Arachis hypogaea L)The experiment was conducted to analyze transcriptional and methylome-induced changes in peanuts under salinity stress. We performed RNA sequencing and whole genome bisulfite sequencing (WGBS) of peanut roots after exposure to 150mM of Nacl for 7 days. A large change in expression was observed in various stress-induced pathways, including the RdDM pathway. ALso, the methylation profile showed an association with the expression of genes involved in stress tolerance.2025-07-07T00:00:00Z2024-02-12T23:48:21.594Z2024-02-12T23:48:21.594ZE-MTAB-13805ERP157418EFO_0002944EFO_0004170EFO_0003789EFO_0002761EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969