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| Status |
Public on Feb 07, 2023 |
| Title |
OE_4_Ip |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: leaves
treatment: cold
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed using the EpiQuiK Plant ChIP kit (Epigentek) as described in the manufacturer’s protocol. Approximately 1.5 g of leaf tissue was harvested from transgenic plants and WT plants, respectively. Chromatin was immunoprecipitated with an HA antibody, and a goat anti-mouse IgG antibody was used as the negative control.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina). Library quality was assessed on the Agilent Bioanalyzer 2100 system.
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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 |
The library was constructed by Novogene Corporation (Beijing, China).
Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina). Library quality was assessed on the Agilent Bioanalyzer 2100 system.
For ChIP-Seq data analysis, raw data of fastq format were firstly processed using fastp (version 0.19.11) software
Clean data were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
After mapping reads to the reference genome, we used the MACS2 (v 2.1.0) peak calling software to identify regions of IP enrichment over background. A adjuested P-value threshold of 0.05 was used for all data sets.
Assembly: Reference genome and gene model annotation files were downloaded from tomato genome website (https://solgenomics.net/) directly.
Supplementary files format and content: bigWig
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| Submission date |
May 12, 2022 |
| Last update date |
Feb 07, 2023 |
| Contact name |
Mingyue Guo |
| E-mail(s) |
21916052@zju.edu.cn
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| Phone |
+8618143465226
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| Organization name |
浙江大学
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| Street address |
浙江大学紫金港校区
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| City |
杭州市 |
| State/province |
浙江省 |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL27957 |
| Series (1) |
| GSE202902 |
SlWRKY33 confers cold tolerance through activation of various downstream signaling pathways in cultivated tomato |
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| Relations |
| BioSample |
SAMN28209272 |
| SRA |
SRX15244405 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6135266_OE_4_IP.bw |
4.3 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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