|
| Status |
Public on Jun 01, 2016 |
| Title |
Colxhalleri Cold biological replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Rossete
|
| Organism |
Arabidopsis thaliana x Arabidopsis halleri |
| Characteristics |
age: 4 weeks
treatment: 4°C for 1 hour
ecotype: Col-0xh2.2
|
| Treatment protocol |
For dehydration, plants were removed from the agar and dehydrated in plastic dishes for 1 hour at 22°C under dim light (0.7±0.8 mmol sec±1 m±2). For cold exposure, plants were grown under dim light(0.7±0.8 mmol sec±1 m±2) at 4°C for 1 hour. Leaf samples of plants growing in non-stressful conditions (standard treatment) were collected on 4 week-old plants grown at 22°C. Each sample was prepared for 3 biological replicates in one week intervals. prepared for 3 biological replicates in one week intervals.
|
| Growth protocol |
A.thalianaxA.lyrata and A.thalianaxA.halleri F1 hybrids were germinated and grown on germination medium (GM) containing Murashige and Skoog salts, 1% sucrose, and 0.8% agar. The plants were stratified for 5 days at 4°C, and then grown for 4 weeks in a growth chamber at 22°C under 16 h light/8 h dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole aerial part of one hybrid individual in 1 mL of TRIZOL Reagent (Thermo Fisher Scientific). DNA was cleaned up using the DNA-free kit (Thermo Fisher Scientific). RNA quality and quantity was examined with the Bioanalyzer 2100 (Agilent) and Qubit® 2.0 Fluorometer (Thermo Fisher Scientific). Two micrograms of Total RNA were used for library preparation.
The library preparation followed the TruSeq® RNA Sample Preparation v2 Guide (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
replicate 2
|
| Data processing |
FastX-toolkit was used for sequence trimming and filtering. Reads were mapping to the concatenation of the A. thaliana Col-0 reference genome (TAIR10, www.arabidopsis.org) and the A. lyrata MN47 reference genome (Araly1,(Nordberg et al. 2014) using tophat2 with -p 5, -N 5, --read-edit-dist 5 --read-gap-length 5. Uniquely and high-quality mapping reads were selected by "samtools view -q 10". Gene expression difference was computed by DESeq2. ASE analysis were calculated by the allele ratios, which fully decribed in the paper.
Supplementary_files_format_and_content: allele-specific levels of expression
|
| |
|
| Submission date |
Apr 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Fei He |
| Organization name |
University of Cologne
|
| Department |
Botanical Institute
|
| Lab |
AG de Meaux
|
| Street address |
Zuelpicher Str. 47 B
|
| City |
Cologne |
| ZIP/Postal code |
50674 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21749 |
| Series (1) |
| GSE80462 |
The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus |
|
| Relations |
| BioSample |
SAMN04873552 |
| SRA |
SRX1715756 |
