NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7844493 Query DataSets for GSM7844493
Status Public on Jul 11, 2024
Title M82 ChIP-seq_H3K4me2 Rep1
Sample type SRA
 
Source name Leaf
Organism Solanum lycopersicum
Characteristics cultivar: M82
genotype: WT
tissue: Leaf
treatment: Non
chip antibody: H3K4me2
bio rep: Bio rep 1
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 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).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
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
 
Submission date Oct 16, 2023
Last update date Jul 11, 2024
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)
GSE245525 KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ChIP-seq]
GSE245529 KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac
Relations
BioSample SAMN37851296
SRA SRX22108262

Supplementary file Size Download File type/resource
GSM7844493_M82_H3K4me2_rep1_p0.05_peaks.broadPeak.gz 1.6 Mb (ftp)(http) BROADPEAK
GSM7844493_coverage_M82_H3K4me2_S10.bigwig 156.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap