GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2454705 Query DataSets for GSM2454705
Status Public on May 19, 2017
Title WT_12hr_rep3
Sample type SRA
Source name WT, 12hr, 2-week-old Arabidopsis seedlings
Organism Arabidopsis thaliana
Characteristics developmental stage: 2-week-old seedlings
genotype: Wild type
ecotype: Col-0
treatment: elf
time: 12 hr
Treatment protocol For elf18 (EZBiolab) treatment, 2-week-old seedlings grown on MS solid medium were transferred to MS liquid medium (pH 5.7) with 1% sucrose and 5 μM elf18 or flg22, and incubated under the same condition and then seedlings were harvested at each time point after peptide application.
Growth protocol Plants of all genotypes were grown on 0.6% agar media containing 0.5x Murashige and Skoog (MS) salts (MP Biomedicals), 1% sucrose (Fisher) and 0.5 g/L MES hydrate (Sigma) in a growth room at 22 oC under 16 h light/8 h dark with white fluorescent light (~100 μmolom-2os-1).
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from Arabidopsis 2-week old seedlings using TRIzol reagent (Ambion), treated with TURBO DNase (Ambion) and purified using RNeasy mini spin column (Qiagen). The quality of purified RNA was assessed using an Agilent 2100 Bioanalyzer.
cDNA libraries for ssRNA-seq were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit according to the low sample protocol guidelines. The quality and size of each sample library was assessed using an Agilent High Sensitivity D1K ScreenTape System. The average sizes of the enriched cDNA fragments were between 272 and 300 bp. The three biological replicates for each condition (negative control, 1 h_elf18, 6 h_elf18, and 12 h_elf18) were pooled into one well, and sequenced on an Illumina NextSeq High Output SR 75 with 75-cycle single reads per multiplexed sample.
Library strategy ssRNA-seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Wild type plants with elf18 treatment, replicate 3 (WT_12hr_rep3)
Data processing Strand-specific RNA-seq reads were mapped to the Arabidopsis genome (TAIR10) using TopHat (version 2.0.8) with parameters “--library-type=fr-firststrand -i 40 -I 5000 -g 1 --segment-length=20”.
The mapped reads were assembled using Cufflinks (v2.1.1) with parameters “--library-type=fr-firststrand -I 5000 --min-intron-length=40” and with TAIR10 annotation as the reference.
The assembled transcripts of each ssRNA-seq sample were merged and annotated using Cuffcompare (v2.1.1) with TAIR10 annotation as the reference.
The expression levels of each gene were then calculated by the fragments per kilobase of exons per million fragments mapped (FPKM) using Cuffdiff with parameter “--library-type=fr-firststrand”.
A 2-fold variance in FPKM, a P value less than 0.05, and an adjusted P value less than 0.1 were used as cutoffs to define differentially expressed genes. The P value and adjusted P value were calculated using DESeq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files include FPKM values and raw read counts of 21,407 protein coding genes
Submission date Jan 12, 2017
Last update date May 15, 2019
Contact name Nam-Hai Chua
Organization name The Rockefeller University
Lab Lab of Plant Molecular Biology
Street address 1230 York Avenue
State/province New York
ZIP/Postal code 10065
Country USA
Platform ID GPL19580
Series (1)
GSE93560 Elf18-induced long noncoding RNA associates with Mediator to enhance expression of innate immune response genes in Arabidopsis
BioSample SAMN06220478
SRA SRX2488349

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap