|
| Status |
Public on Mar 11, 2021 |
| Title |
At_M_R3_1h |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis thaliana Col-0
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedling
age: 12 day old
treatment: mock
timepoint: 1h
replicate: r3
|
| Treatment protocol |
Eleven-day-old seedlings were transferred from ½ MS-Agar to 24-well plates each with 1.6 ml of ½ MS-Medium 24 h prior to treatments. Five to ten seedlings were transferred per well. For the flg22 treatment 800 µl of 3 µM flg22 solution was added to the medium containing the seedlings resulting in a final concentration of 1 µM flg22. For mock treatments 800 µl 1/2 MS medium was added to the wells. Three well were combined to create one sample.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
seedlings were flash frozen in liquid nitrogen and RNA was extracted using peqGOLD TriFast reagent
library preparation was performed with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: merged_counts_Ath.txt
|
| Data processing |
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to A. thaliana (TAIR10), C. hirsuta (http://chi.mpipz.mpg.de/), C. rubella (Phytozome 10), E. salsugineum (Phytozome10) or individual A. thalianna accession genomes corrected for SNPs usingTopHat2 (v2.1.1) with following parameters: --read-mismatches 10 --read-gap-length 10 --read-edit-dist 20 --read-realign-edit-dist 0 --min-anchor 5 --splice-mismatches 2 --min-intron-length 30 --max-intron-length 10000 --max-insertion-length 20 --max-deletion-length 20 --num-threads 10 --max-multihits 10 --coverage-search --library-type fr-firststrand --segment-mismatches 3 --min-segment-intron 30 --max-segment-intron 10000 --min-coverage-intron 30 --max-coverage-intron 10000 --b2-very-sensitive
reads per gene were counted using HtSeq (v 0.6.0) with default parameters
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.
|
| |
|
| Submission date |
Jun 19, 2018 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Kenichi Tsuda |
| E-mail(s) |
tsuda@mail.hzau.edu.cn, tsuda@mpipz.mpg.de
|
| Organization name |
Huazhong Agricultural University
|
| Lab |
Kenichi Tsuda
|
| Street address |
No.1 Shizishan Road
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE115991 |
Flg22 treatment of Brassicaceae and Arabidopsis thaliana accessions |
|
| Relations |
| BioSample |
SAMN09453440 |
| SRA |
SRX4236169 |
