|
| Status |
Public on Dec 02, 2024 |
| Title |
PHILO, TC, Col-0, H3K4me3, 2hJA, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
10-day-old whole seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 10-day-old whole seedling
chip antibody: anti-H3K4me3 (#04-475, Millipore Sigma)
genotype: Col-0
treatment: 2h JA
|
| Treatment protocol |
Seedlings were either untreated or treated for the indicated hours with gaseous MeJA.
|
| Growth protocol |
Arabidopsis seedlings were grown for 10 days under long day conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Seedlings were crosslinked with 1% formaldehyde solution for 2 x 10 min. After quenching, samples were shock-frozen, ground and chromatin was subsequently extracted. Chromatin was sonicated with a Diagenode Bioruptor.
Libraries were prepared as follows. End repair (5 μl of End Repair Reaction Buffer + 2.5 μl of End Repair Enzyme Mix from the NEBNext End Repair Module (New England Biolabs)), A-tailing (2.5 µl NEBnext dA-Tailing Reaction Buffer + 1.5 µl Klenow Fragment (3'5' exo-) (New England Biolabs)), adapter ligation(1 µl TruSeq DNA Unique Dual Indexes (UDIs) v2 (Illumina), 2.5 µl T4 DNA Ligase Reaction Buffer + 1.25 µl T4 DNA Ligase (New England Biolabs)), and PCR enrichment (12.5 µl NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie2 (version 2.4.1).
To generate ChIP-seq coverage plots, bamCoverage (binSize 5) from deepTools (version 3.5.2) was used.
Histone marks domains were identified with epic2 (version 0.0.52) using default parameters and Col-0 IgG samples as controls.
MYC2 DNA binding peaks were identified with MACS2 (version 2.2.7.1) by comparing two biological replicates of untreated (ctrl) and 2 h JA-treated myc2 MYC2:MYC2-FLAG seedlings.
Assembly: TAIR10
Supplementary files format and content: bigwig, narrowPeak, domain.csv
|
| |
|
| Submission date |
Dec 08, 2023 |
| Last update date |
Dec 02, 2024 |
| Contact name |
Mark Zander |
| E-mail(s) |
[email protected]
|
| Organization name |
Rutgers State University of New Jersey
|
| Street address |
190 Frelinghuysen Rd
|
| City |
Piscataway |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE249736 |
High-throughput capture of transcription factor-driven chromatin dynamics using PHILO ChIP-seq (ChIP-seq) |
| GSE249738 |
High-throughput capture of transcription factor-driven chromatin dynamics using PHILO ChIP-seq |
|
| Relations |
| BioSample |
SAMN38732477 |
| SRA |
SRX22834645 |
