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| Status |
Public on Aug 05, 2024 |
| Title |
Mutant fourth leaves,1-month-old,H3K9ac |
| Sample type |
SRA |
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| Source name |
1-month-old leaves
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| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: 1-month-old leaves
genotype: ddm1 mutant
chip antibody: H3K9ac
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| Growth protocol |
M82 and ddm1 seeds were germinated on soil and plants were grown in growth chamber at 24°C with a 16/8h light and dark period
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq assays were performed according to Ramirez-Prado et al. (Ramirez-Prado et al, 2021) with extra modifications to the chromatin extraction step cross-linked plants were ground using gentleMACS (Miltenyi Biotec) with the 4C program in an extraction buffer (50mM HEPES-KOH pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS) containing protease inhibitors. The mixture was filtered through a 50µm filter and left on ice for 10 minutes. After centrifuge for 10 minutes at 1500g at 4°C, the supernatant was removed and the pellet was resuspended in sonication buffer (50mM HEPES KOH pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.2% SDS) containing protease inhibitors. 4ug of anti-H3K9me2 (Abcam, ab1220), anti-H3K27me1 (Millipore, 07–448), and anti-H3K27me3 (Millipore, 07-449) antibodies were used.
ChIP-seq libraries were prepared from 10 ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.
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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 M82 V1.0 genome.
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 MACS3.0.0a6 with the command "macs3 callpeak -t sample.bam -c Input.bam -g 829069930 -q 0.05 -B -n --outdir "
Bigwig generation: read density was scored with s3norm with the default paramaters
Assembly: M82 V1.0
Supplementary files format and content: bigWig, broadPeak
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| Submission date |
Apr 30, 2024 |
| Last update date |
Aug 05, 2024 |
| Contact name |
Xiaoning HE |
| E-mail(s) |
[email protected]
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| Organization name |
IPS2
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| Street address |
630 Rue Noetzlin
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| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
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| Platform ID |
GPL21762 |
| Series (2) |
| GSE243908 |
THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION [ChIP-seq] |
| GSE243911 |
THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION |
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| Relations |
| BioSample |
SAMN41135906 |
| SRA |
SRX24410734 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8244457_ChIP_ddm1_K9ac_S8.s3norm.bigwig |
235.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM8244457_ddm1_K9ac_q005_peaks.narrowPeak.gz |
1.8 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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