|
| Status |
Public on Dec 09, 2018 |
| Title |
WTa |
| Sample type |
SRA |
| |
|
| Source name |
14 day-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: ColO
treatment: untreated
tissue: 14 day-old seedlings
|
| Treatment protocol |
1µM flg22 treatment for 1 hour
|
| Growth protocol |
14 day-old seedlings were grown under long-day conditions on sugar-free MS (Murashige and Skoog) plates at 23oC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The whole 14 day-old seedlings were used for total RNA extraction. ChIP assays were performed on 14 day-old in half MS-grown seedlings using Anti-GFP antibody - ChIP Grade (Abcam) and RNA polymerase II (Santa Cruz) antibodies. Briefly, after plant material fixation in 1% (v/v) formaldehyde, the tissues were homogenised, and the nuclei were isolated and lysed. Cross-linked chromatin was sonicated using a water bath Bioruptor UCD-200 (Diagenode; 15-s on/15-s off pulses, 15 times). The complexes were immunoprecipitated with antibodies overnight at 4°C with gentle shaking and incubated for 1 h at 4°C with 50 μL of Dynabeads Protein A (Invitrogen).
mRNA library generation followed by paired end sequencing (Hiseq4000). NEB ChIP-seq Library Prep Master Set for Illumina
Sequencing was performed on each library to generate 101-bp paired-end reads on Illumina HiSeq Genome Analyzer platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequenced reads were processed using Trimmomatic to remove adapter contents and low quality bps.
ChipSeq reads were mapped to TAIR10 genome using bowtie2.
RNAseq reads were mapped to TAIR10 genome using TOPHAT.
Chipseq peaks were calculated using MACS2.
RNSeq diffential expression was done using cufflinks package.
Genome_build: TAIR10
Supplementary_files_format_and_content: wiggle, excel
|
| |
|
| Submission date |
Sep 17, 2018 |
| Last update date |
Dec 09, 2018 |
| Contact name |
Prof. Heribert HIRT |
| Organization name |
KAUST
|
| Street address |
4700 KAUST
|
| City |
Thuwal |
| ZIP/Postal code |
239556900 |
| Country |
Saudi Arabia |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE120068 |
INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana. |
|
| Relations |
| BioSample |
SAMN10079193 |
| SRA |
SRX4704979 |
