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| Status |
Public on Aug 30, 2021 |
| Title |
G1812_ChIPseq_AP2-DREB-7 |
| Sample type |
SRA |
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| Source name |
Triticum urartu seedling
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| Organism |
Triticum urartu |
| Characteristics |
antibody: Flag
antibody manufacturer: sigma
accession: G1812 (PI428198)
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| Treatment protocol |
For ABA treatments, 7-day-old seedlings grown in soil were treated with 100 μm ABA for 2 weeks.
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| Growth protocol |
16h light, 8h dark, 22°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For histone ChIP-seq assay, approximately 30 seedlings were pooled and ground to a powder. More than 10 ng ChIP DNA was used to prepare each sequencing sample. For TF ChIP-seq assay, Tu plants grown on soil under 16 h light/ 8 h dark conditions for 2 weeks before protoplast isolation. Approximately, 30 ug pMD19-T plasmids containing p35S:3flag-AP2 DNA were transfected into leaf protoplasts using the PEG-mediated transfection method. After incubating the protoplasts at room temperature for 48 h under dark condition, the protoplasts were crosslinked with 1% formaldehyde in W5 solution for 10 min on ice and quenched with 32 ul 2 M glycine for 5 min. Protoplasts were collected by centrifuging at 600 g for 2 min at 4°C, wash with 500 ul W5 solution once and collected again. Protoplasts were lysed in 120 ul room temperature lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (wt/vol) SDS, 1 mM PMSF, 1× protease inhibitor cocktail) by vortex. Total lysates containing chromatin were subjected to sonication by Bioruptor until the chromatin was fragmented into 300bp-500bp.
Libraries were prepared for sequencing using standard Illumina protocols.
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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 |
Sequencing reads were cleaned with the Trim Galore, Trimmomatic, and Sickle programs.
The cleaned reads were mapped to WheatTu IGDBv1.0 using BWA.
MACS was used to identify read-enriched regions (peaks) with P value < 1e–10.
Genome_build: IGDBv1.0
Supplementary_files_format_and_content: peak files and bigwig files
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| Submission date |
Aug 24, 2021 |
| Last update date |
Aug 30, 2021 |
| Contact name |
yijing zhang |
| E-mail(s) |
zhangyijing@fudan.edu.cn
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| Organization name |
Fudan University
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| Department |
Biochemistry
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| Lab |
Functional Epigenomics Group
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| Street address |
2005 Songhu Road
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| City |
shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| Platform ID |
GPL29754 |
| Series (2) |
| GSE167229 |
Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements |
| GSE182693 |
Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements [ChIP-Seq] |
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| Relations |
| BioSample |
SAMN20962148 |
| SRA |
SRX11897710 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5534765_G1812_ChIP_AP2-DREB-7.bw |
200.6 Mb |
(ftp)(http) |
BW |
| GSM5534765_G1812_ChIP_AP2-DREB-7_peaks.xls.gz |
706.8 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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