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Sample GSM8267279 Query DataSets for GSM8267279
Status Public on Dec 02, 2024
Title PHILO, Tomato, H3K9ac, 2hJA, rep2
Sample type SRA
 
Source name two-week-old whole seedling
Organism Solanum lycopersicum
Characteristics chip antibody: anti-H3K9ac (39137, Active Motif)
genotype: Micro-Tom
treatment: none
Treatment protocol no treatment
Growth protocol Ten-day-old Col-0 Arabidopsis seedlings, two-week-old Micro-Tom tomato (Solanum lycopsericum) seedlings, and two-week-old Otto II Boax hemp (Cannabis sativa)seedlings grown under a 16 h light/8 h dark cycle were used for PHILO ChIP-seq analysis.
Extracted molecule genomic DNA
Extraction protocol Tissues were crosslinked with 1% formaldehyde solution for 2 x 10 min. After quenching, samples were shock-frozen, ground and chromatin was subsequently extracted. Chromatin was sonicated with a Diagenode Bioruptor.
Libraries were prepared as follows. End repair (5 μl of End Repair Reaction Buffer + 2.5 μl of End Repair Enzyme Mix from the NEBNext End Repair Module (New England Biolabs)), A-tailing (2.5 µl NEBnext dA-Tailing Reaction Buffer + 1.5 µl Klenow Fragment (3'5' exo-) (New England Biolabs)), adapter ligation(1 µl TruSeq DNA Unique Dual Indexes (UDIs) v2 (Illumina), 2.5 µl T4 DNA Ligase Reaction Buffer + 1.25 µl T4 DNA Ligase (New England Biolabs)), and PCR enrichment (12.5 µl NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq reads were aligned to the TAIR10 (Arabidopsis thaliana), SLM_r2.0.pmol (Solanum lycopersicum), cs10 (Cannabis sativa) using Bowtie2 (version 2.4.1).
To generate ChIP-seq coverage plots, bamCoverage (binSize 5) from deepTools (version 3.5.2) was used.
Histone marks domains were identified with epic2 (version 0.0.52) using default parameters and IgG samples as controls.
Assembly: TAIR10 (Arabidopsis thaliana), SLM_r2.0.pmol (Solanum lycopersicum), cs10 (Cannabis sativa)
Supplementary files format and content: bigwig, domain.csv
 
Submission date May 14, 2024
Last update date Dec 02, 2024
Contact name Mark Zander
E-mail(s) [email protected]
Organization name Rutgers State University of New Jersey
Street address 190 Frelinghuysen Rd
City Piscataway
ZIP/Postal code 08854
Country USA
 
Platform ID GPL21762
Series (2)
GSE249738 High-throughput capture of transcription factor-driven chromatin dynamics using PHILO ChIP-seq
GSE267486 High-throughput capture of transcription factor-driven chromatin dynamics using PHILO [ChIP-seq 3]
Relations
BioSample SAMN41396950
SRA SRX24550133

Supplementary file Size Download File type/resource
GSM8267279_Tomato_H3K9ac_2hJA_rep2.bw 60.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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