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Sample GSM8080427 Query DataSets for GSM8080427
Status Public on Aug 31, 2024
Title Mite-infested, 4 d, rep 1
Sample type SRA
 
Source name aerial plant tissue from four plants pooled
Organism Arabidopsis thaliana
Characteristics tissue: aerial plant tissue from four plants pooled
ecotype: Columbia (col-0)
treatment: Mites
treatment time: 4 d
Treatment protocol Three-week-old Arabidopsis plants were infested with twenty T. urticae female adults per plant. Plant aerial material was sampled at specific ontological stages of the plant development, coinciding with 30 min, 24 h, 4 d, 7 d, 12 d and 15 d post-mite infestation. Plant material was introduced in liquid nitrogen and stored at -80ºC until used for RNA extraction.
Growth protocol Sterilized seeds were planted in a mixture of peat moss and vermiculite (3:2 v/v) and incubated in the dark for 5 days at 4°C. Plants were then transferred to growth chambers (Aralab D1200PLH) under controlled conditions (23°C ± 1°C, >70% RH and a 16 h/8 h day/night photoperiod).
Extracted molecule total RNA
Extraction protocol Frozen material was thoroughly grinded on liquid nitrogen and total RNA was extracted by means of the RNeasy plant mini kit (Qiagen), and a DNase treatment (Qiagen) following manufacturer´s instructions.
RNA libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Libraries were sequenced on an Illumina platform generating paired-end reads fragments of 150 bp.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description M4.1
Data processing Raw data (reads) obtained as FASTQ files were processed to remove adapters, poly-N sequences and reads with low quality from raw data using fastp. Quality of the resulting data was assessed by the evaluation of Q20, Q30 and GC content. Paired-end clean reads were mapped against the TAIR10 reference genome of A. thaliana using HISAT2 software. Quality of the mapping was also checked. FeatureCounts was used for the generation of the count data files from sorted BAM files
Differential expression analysis comparing treated against control samples at each time point was performed using DESeq2 R package. P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Differentially expressed genes (DEGs) were considered when p-value adjusted < 0.05 and log2FC > |1| were present. Fold change data can be accessed directly from the publication.
Assembly: TAIR 10 reference genome
Supplementary files format and content: tab delimited tsv file containing raw counts for each Sample
 
Submission date Feb 14, 2024
Last update date Aug 31, 2024
Contact name Alejandro García
E-mail(s) alejandro.garciagar@upm.es
Organization name Universidad Politécnica de Madrid
Street address Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38
City Madrid
ZIP/Postal code 28223
Country Spain
 
Platform ID GPL17639
Series (1)
GSE255811 TRANSCRIPTIONAL AND HORMONAL DEFENCE-GROWTH TRADEOFFS DETERMINE PLANT SURVIVAL AND FITNESS UPON SPIDER MITE INFESTATION
Relations
BioSample SAMN39946417
SRA SRX23622530

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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