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| Status |
Public on Jan 03, 2023 |
| Title |
M82-HS-0h ChIP-seq_H3K9ac Rep1 |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: cv. M82 (Tomato cultivar M82)
genotype: WT
tissue: Leaf
treatment: Heat stress 0h
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| Treatment protocol |
4 weeks old plants were treated at 45°C 0h, 1h and 6h in the climatic chamber (aralab).
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| Growth protocol |
Plants were grown in pots in growth chambers at 24 °C under long-day (16 h of light) conditions.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq assays were performed on 4-week-old tomato fourth branch of leaves according to Bio-protocol of Ramirez-Prado, J.S. et al (2021) by using anti-H3K27me1 (Millipore, 07-448), anti-H3K9ac (Millipore, 07-352), anti-H3K14ac (Millipore, 07-353), anti-H3K18ac (Millipore, 07-354), anti-H3K27ac (Abcam, ab4729), anti-H3K4me3 (Millipore, 07-473) and anti-polymerase II (Abcam, ab26721) antibodies.
ChIP-seq libraries were prepared from 10ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions. Two independently biological replicates were generated for each time point of heat stress. DNA libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Bio rep 1
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| Data processing |
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30 "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak -t sample.bam -c Input.bam -g 829069930 -p 0.05 --extsize 150 --bw 500 -B -n --outdir
Bigwig generation: read density was scored with s3norm with the default paramaters
Assembly: SollycM82_v1.0
Supplementary files format and content: s3norm normalized bigwig for plots generated with ComputeMatrix plotprofile of Deeptools
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| Submission date |
Jun 17, 2022 |
| Last update date |
Jan 04, 2023 |
| Contact name |
Jing An |
| Organization name |
Universite Paris Saclay
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| Street address |
630 Rue Noetzlin
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| City |
Paris |
| ZIP/Postal code |
91190 |
| Country |
France |
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| Platform ID |
GPL21762 |
| Series (2) |
| GSE206358 |
HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [ChIP-seq] |
| GSE206365 |
HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions. |
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| Relations |
| BioSample |
SAMN29178782 |
| SRA |
SRX15782142 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6252567_M82_0h_H3K9ac_rep1_p0.05_peaks.narrowPeak.gz |
2.0 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM6252567_M82_0h_H3K9ac_rep1_s3norm.bigwig |
314.0 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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