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| Status |
Public on Dec 02, 2024 |
| Title |
PHILO, Arabidopsis, H3K9ac, sonic_0.1g, rep2 |
| Sample type |
SRA |
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| Source name |
10-day-old whole seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
chip antibody: anti-H3K9ac (39137, Active Motif)
genotype: Col-0
treatment: none
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| Treatment protocol |
no treatment
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| 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.
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| 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).
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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 |
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
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| Submission date |
May 14, 2024 |
| Last update date |
Dec 02, 2024 |
| Contact name |
Mark Zander |
| E-mail(s) |
[email protected]
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| Organization name |
Rutgers State University of New Jersey
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| Street address |
190 Frelinghuysen Rd
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| City |
Piscataway |
| ZIP/Postal code |
08854 |
| Country |
USA |
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| Platform ID |
GPL19580 |
| 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] |
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| Relations |
| BioSample |
SAMN41396969 |
| SRA |
SRX24550113 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8267260_PHILO_H3K9ac_sonic_0.1g_rep2.bw |
28.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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