|
| Status |
Public on Jul 10, 2021 |
| Title |
jmj7_H3K4me3_ChIPSeq_IP rep2 |
| Sample type |
SRA |
| |
|
| Source name |
jmj7_H3K4me3_ChIPSeq_IP
|
| Organism |
Solanum lycopersicum |
| Characteristics |
background: Ailsa Craig
genotype/variation: jmj7
develpmental stage: At 38 days after anthesis (dpa)
tissue: Pericarp
chip antibody: H3K4me3 (ab8580, Abcam)
|
| Growth protocol |
Wild-type tomato and transgenic lines in the Ailsa-Craig background were grown in a greenhouse at 23°C under 16 h light and 8 h dark condition.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Pericarp at the equatorial part of the fruit were collected, immediately cross-linked in 1% formaldehyde for chromatin isolation and Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to Tomato reference genome (version SL3.0) using the BWA program.
Peaks were called using MACS2 software with the following setting: MACS2 callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B –SPMR --broad --broad-cutoff 0.05.
Genome_build: Tomato reference genome (version SL3.0)
Supplementary_files_format_and_content: bigwig files were generated using MACS2 software.
|
| |
|
| Submission date |
Apr 12, 2020 |
| Last update date |
Jul 10, 2021 |
| Contact name |
Ding xiaochun |
| E-mail(s) |
dingxc111@scbg.ac.cn
|
| Organization name |
SOUTH CHINA BOTANICAL GARDEN
|
| Street address |
723 xingke road, tianhe district
|
| City |
guangzhou city |
| State/province |
guangdong |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL27957 |
| Series (2) |
| GSE148525 |
Histone demethylase SlJMJ7 Integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato [ChIP-seq] |
| GSE148527 |
Histone demethylase SlJMJ7 integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato. |
|
| Relations |
| BioSample |
SAMN14588137 |
| SRA |
SRX8110016 |
