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| Status |
Public on Jul 11, 2024 |
| Title |
M82 ChIP-seq_H3K4me1 Rep1 |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: M82
genotype: WT
tissue: Leaf
treatment: Non
chip antibody: H3K4me1
bio rep: Bio rep 1
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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 aAnti-RNAPII (Abcam, ab26721), Anti-H3K4ac (Active Motif, 39382), Anti-H3K4me3 H3K4me3 (Millipore 07-473), Anti-H3K4me2 (active motif, 39142), Anti-H3K4me1 (active motif, 39300), Anti-H3K9ac (Millipore, 07-352), Anti-H3K9me2 (Abcam, ab1220), Anti-H3K14ac (Millipore, 07-353), Anti-H3K14me1 (Active Motif, 61510), Anti-H3K18ac (Millipore, 07-354), Anti-H3K23me3 (Active Motif, 61500), Anti-H3K23me1 (Active Motif, 39388), Anti-H3K27ac (Abcam, ab4729), Anti-H3K27me3 (Millipore 07-449), Anti-H3K27me2 (Abcam, 24684), Anti-H3K27me1 (Millipore, 07-488), Anti-H3K36ac (Active Motif, 39380), Anti-H3K36me3 (Abcam, ab9050), Anti-H3K56ac (Active Motif, 39282), Anti-H3K56me2 (Active Motif, 39278), Anti-H3K56me1 (Active Motif, 39274), Anti-H3K79ac (Active Motif, 39566), Anti-H4K5ac (Active Motif, 39700), Anti-H4K8ac (Active Motif, 61104), Anti-H4K12ac (Active Motif, 61531), Anti-H4K16ac (Active Motif, 39930), Anti-H4K20ac (Active Motif, 61531) 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. 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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| 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 (with respectively narrow or broad mode)
Bigwig generation: read density was scored with deeptools the default bamCoverage paramaters
Assembly: SollycM82_v1.0
Supplementary files format and content: Bamcoverage bigwig for plots generated with ComputeMatrix plotprofile of Deeptools
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| Submission date |
Oct 16, 2023 |
| Last update date |
Jul 11, 2024 |
| 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) |
| GSE245525 |
KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ChIP-seq] |
| GSE245529 |
KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac |
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| Relations |
| BioSample |
SAMN37851297 |
| SRA |
SRX22108261 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7844492_M82_H3K4me1_Input_p0.05_peaks.narrowPeak.gz |
820.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM7844492_coverage_M82_H3K4me1_rep1_S11.bigwig |
167.8 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
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