|
| Status |
Public on May 19, 2017 |
| Title |
WT_12hr_rep2 |
| 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 2 (WT_12hr_rep2)
|
| 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
|
| City |
NEW YORK |
| 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 |
|
| Relations |
| BioSample |
SAMN06220479 |
| SRA |
SRX2488348 |
