|
| Status |
Public on Jan 03, 2023 |
| Title |
HiC_M82_HS_1h_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: cv. M82 (Tomato cultivar M82)
genotype: WT
tissue: Leaf
treatment: Heat stress 1h
|
| Treatment protocol |
4 weeks old plants were treated at 45°C for 0h, 1h and 6h in a climatic chamber (Aralab).
|
| Growth protocol |
Plants were grown in pots in growth chambers at 24 °C under long-day (16 h of light) conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ Hi-C experiments were performed according to Concia et al (2020) using DpnII enzyme (New England Biolabs).
DNA libraries were prepared using NEBNext Ultra II DNA library preparation kit (NEB) according to the manufacturer’s instructions (10 cycles for the PCR amplification step). DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and the libraries were subjected to 2 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Bio rep 1
|
| Data processing |
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar PE $input1 $input2 $output1Paired $output1Unpaired $output2Paired $output2Unpaired ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using HiC-Pro v 2.11.4 with the following setting "BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.6 --end-to-end --reorder BOWTIE2_LOCAL_OPTIONS = --very-sensitive -L 20 --score-min L,-0.6,-0.6 --end-to-end --reorder GENOME_FRAGMENT = SollycM82_v1.0_dpnii.bed" against the genome of SollycM82_v1.0.
Assembly: SollycM82_v1.0
Supplementary files format and content: allValidPairs.txt files for generating contact matrices
|
| |
|
| Submission date |
Jun 17, 2022 |
| Last update date |
Jan 04, 2023 |
| Contact name |
Jing An |
| Organization name |
Universite Paris Saclay
|
| Street address |
630 Rue Noetzlin
|
| City |
Paris |
| ZIP/Postal code |
91190 |
| Country |
France |
| |
|
| Platform ID |
GPL21762 |
| Series (2) |
| GSE206360 |
HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [Hi-C] |
| GSE206365 |
HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions. |
|
| Relations |
| BioSample |
SAMN29179767 |
| SRA |
SRX15782237 |
