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| Status |
Public on Jun 17, 2022 |
| Title |
YZ, H3K9me2, rep2 input |
| Sample type |
SRA |
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| Source name |
Young Leaves
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| Organism |
Capsicum annuum |
| Characteristics |
cultivar: cv. 59
tissue: Young Leaves
chip antibody: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Grind young leaf (2g) into a fine powder in liquid nitrogen and then crosslinked with 1% formaldehyde for 10 min at room temperature.
After sonication, immunoprecipitation was performed with antibodies. ChIP was performed using antibodies against the following: H3K4me3 (Abcam, ab8580), H3K27me3 (Millipore 07-499), and H3K9me2 (Abcam, ab1220). The immunoprecipitated complex was washed, and DNA was extracted and purified by Universal DNA Purification Kit (QIAquick PCR Purification Kit, 28106). The ChIP-Seq library was prepared using the ChIP-Seq DNA sample preparation kit (NEBNext® Ultra™II DNA) according to the manufacturer’s instructions. For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Illumina Novaseq 6000 using 150bp paired-end. Samples were prepared and sequenced with assistance from Shanghai Jiayin Biotechnology Co., Ltd.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
ChIP-seq reads were trimmed using Trimmomatic 0.38 with the parameter SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 ILLUMINACLIP:adapters.fa:2:30:7:1:true MINLEN:36
ChIP-seq reads were aligned to Ca_59 genome using bwa version 0.7.17.
Enrichment peaks were called using MACS2 (2.2.7.1) with default parameters.
The ChIP-seq intensity of a genomic bin (i.e. 10 kb and 40 kb) was calculated using the bamCoverage tool from DeepTools (3.3.0) with the read coverage normalized in CPM.
Assembly: Ca_59/GCA_021292135.1
Supplementary files format and content: bedgraph
Supplementary files format and content: bigWig, narrowPeak
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| Submission date |
Jun 13, 2022 |
| Last update date |
Jun 17, 2022 |
| Contact name |
Juntao Wang |
| E-mail(s) |
[email protected]
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| Organization name |
South China Agricultural University
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| Department |
Collage of Horticulture
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| Street address |
Wushan Street
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510642 |
| Country |
China |
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| Platform ID |
GPL29650 |
| Series (1) |
| GSE206031 |
The 3D architecture of the pepper genome and its relationship to function and evolution |
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| Relations |
| BioSample |
SAMN26112922 |
| SRA |
SRX14237136 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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