|
| Status |
Public on Sep 03, 2020 |
| Title |
Drought_D_R1 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genetic accession: Columbia-0 (Col-0)
abiotic stress: Drought
age: 10 day old
|
| Treatment protocol |
heat (38C for 6h), cold (4C for 24h), salt (250mM Nacl for 6h) and drought(air dry 1h)
|
| Growth protocol |
Pants were grown on 1/2MS plate with 3% sucrose for 10 days before giving stress
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For RNA-seq, total RNA was extracted with Qiagen plant RNA extraction kit. For Dnase-seq, Nuclei were extracted using protocol deescribed by Dorweiler et al 2000 followed by Dnase I digestion as described by He et al 2012. For FAIRE-seq, seedlings were fixed with formaldehyde before extracting nuclei and chromatin was extracted as described by Giresi et al 2007.
DNA library were prepared with NEB kit whereas RNA-seq was prepared as per protocol of Illumina TruSeq RNA sample preparation kit.
50 bp single end on Illumina HiSeq 2000
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Drought_D_macs2_peaks.narrowPeak
|
| Data processing |
Library strategy: Dnase-seq
FASTQC for quality control
Bowtie2/Tophat2 for mapping to TAIR 10
Samtools for pre-processing
MACS2 for peak calling
Cufflink, cummerband for RNA-seq
Genome_build: TAIR10
Supplementary_files_format_and_content: narrow peak containing coordinates of the open chromatin region with tag density
|
| |
|
| Submission date |
Feb 21, 2020 |
| Last update date |
Sep 03, 2020 |
| Contact name |
Vivek Kumar Raxwal |
| E-mail(s) |
vivek.raxwal@ceitec.muni.cz
|
| Organization name |
Central European Institute of Technology
|
| Department |
Plant Molecular Biology
|
| Street address |
building A26, Kamenice 753/5
|
| City |
Brno |
| ZIP/Postal code |
62500 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE145742 |
Landscape of open chromatin regions in Arabidopsis upon exposure to abiotic stresses |
|
| Relations |
| BioSample |
SAMN14162608 |
| SRA |
SRX7780576 |
