|
Status |
Public on Sep 03, 2020 |
Title |
Control_F_R3 |
Sample type |
SRA |
|
|
Source name |
seedlings
|
Organism |
Arabidopsis thaliana |
Characteristics |
genetic accession: Columbia-0 (Col-0) abiotic stress: Control 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
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|
|
Library strategy |
FAIRE-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Control_F_macs2_peaks.narrowPeak
|
Data processing |
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
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|
|
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 |
SAMN14162586 |
SRA |
SRX7780555 |