|
| Status |
Public on Mar 15, 2024 |
| Title |
Seedling, 3d at 4°C, H3K4me3, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Whole seedlings
genotype: Wild type
condition: 4degree C
time: 3d
antibody: H3K4me3 (C15410003, Diagenode)
|
| Treatment protocol |
Plants were cold treated at 4°C in short day conditions for 3h or 3d.
|
| Growth protocol |
Arabidopsis thaliana plants were grown for 21 days in short days (8h light, 16h dark) at 20°C, on 1/2MS plates with 1.5% agar.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each replicate, 1g of seedlings was crosslinked with PFA and chromatin was extracted as described in Vyse et al. (2020). The chromatin was immunoprecipitated using 1 μg of α-H3K27me3 (C15410195 Diagenode) or α-H3K4me3 (C15410003, Diagenode).
DNA was purified and concentrated using the ChIP DNA Clean and Concentrator lit (Zymo Research). The libraries were prepared using the ThruPLEX DNA-seq kit (Takara Bio) and indexes from the SMARTer DNA HT Dual Index kit (Takara Bio). DNA fragments were then selected based on size using AMPure beds (Beckman Coulter). The concentration of the samples was measured using the Qubit dsDNA High Sensitivity kit and the Qubit Fluorometer (ThermoFisher Scientific) and the library quality was assessed using the High Sensitivity DNA ScreenTape and the TapeStation (Agilent).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The reads were mapped to the TAIR10 reference genome of Arabidopsis thaliana using Bowtie2
PCR duplicates and reads with an aligment quality MAPQ < 10 were removed using samtools rmdup and samtools view
peak calling was performed using MACS2, using the broad option and a p-value threshold of 0.01
Bigwig tracks were generated by pooling the two replicates and normalizing as RPKM using DeepTools bamCoverage, using a bin size of 10bp
Assembly: TAIR10
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak (except for input samples)
|
| |
|
| Submission date |
Feb 09, 2024 |
| Last update date |
Mar 15, 2024 |
| Contact name |
Lea Andree Charlotte Faivre |
| Organization name |
Freie Universitaet Berlin
|
| Department |
Biologie, Chemistry, Pharmacy
|
| Lab |
Epigenetics of Plants
|
| Street address |
Königin Luise Str. 12-16
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23157 |
| Series (2) |
| GSE255444 |
Cold stress induces a rapid redistribution of the antagonistic marks H3K4me3 and H3K27me3 in Arabidopsis thaliana [ChIP-Seq] |
| GSE255445 |
Cold stress induces a rapid redistribution of the antagonistic marks H3K4me3 and H3K27me3 in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN39898651 |
| SRA |
SRX23584551 |
