|
| Status |
Public on Mar 13, 2020 |
| Title |
Col-0_JA_0hour_RNAseq_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Three day old etiolated seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Three day old etiolated seedlings
genotype: Col-0
treatment: JA treatment for 0h
|
| Treatment protocol |
JA treatment in time series 0-24 h
|
| Growth protocol |
Seeds were sterilised using bleach then plated on 1.2% agar Linsmaier and Skoog medium plates. Stratification was at 4 celsius in the dark for three days. Plates were exposed to the light at room temperature for 2 h to induce germinaiton, then returned to the dark at 22 celsius. Plates were incubated for three days, after which treatments were conducted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Plant Mini Kit (74903, Qiagen)
cDNA library preparation and subsequent single read sequencing was carried as previously described (Song,L et al., 2016) DOI: 10.1126/science.aag1550
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNASeq_Sample 3
|
| Data processing |
base-calling using RTA 2.7.7
Sequencing reads were quality trimmed using TrimGalore 0.4.5, then aligned to the TAIR10 genome assembly using TopHat 2.1.1
Reads were counted using HTSeq. Differentially expressed genes were identified using edgeR 3.6.2
Quantification of transcripts was performed using Salmon v0.8.1
The TSIS R package was used to perform the isoform switch analysis
Genome_build: TAIR10 and AtRTD2-QUASI
Supplementary_files_format_and_content: csv files include readcount and TPM values for each Sample
|
| |
|
| Submission date |
Jul 18, 2019 |
| Last update date |
Mar 14, 2020 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE133408 |
The jasmonate-response genome regulatory program is defined by the direct targets of transcription factors MYC2 and MYC3, chromatin modification and gene expression changes |
|
| Relations |
| BioSample |
SAMN12308569 |
| SRA |
SRX6460076 |
