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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 12, 2022 |
| Title |
AP2-ERF-6A-1_rep2 |
| Sample type |
SRA |
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| Source name |
Triticum aestivum seedling
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| Organism |
Triticum aestivum |
| Characteristics |
dap antibody: Halo
antibody manufacturer: Promega
antibody catalog #: G7281
cultivar: Chinese Spring
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| Growth protocol |
16h light, 8h dark, 22°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from leaves using Plant DNAzol Reagent(invitrogen). RNA was extracted using TRIzol.
Genomic DNA was fragmented. And then end repaired using the End-It kit(Lucigen) and A-tailed using Klenow(3′–5′ exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase(Promega). Full length TF was cloned into pIX-Halo vector. Halo-tagged TF was expressed in vitro using TNT SP6 Coupled Wheat Germ Extract System(Promega). Halo-TF was immobilized by Magne HaloTag Beads(Promega) and then incubated with the DNA library. TF specific binding DNA was eluted for 10 min at 98°C and amplified with indexed Illumina primer using Phanta Max Super-Fidelity DNA Polymerase(Vazyme). Meanwhile, to capture background DNA which captured by Halo, pIX-Halo vector without TF cloned was expressed and incubated with the DNA library as well. The PCR product was purified using VAHTS DNA Clean Beads(Vazyme).
DAP-seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequencing reads were cleaned with the fastp(version 0.20.0) and Trim Galore (version 0.4.4), which eliminated bases with low quality scores(< 25) and irregular GC contents, sequencing adapters, and short reads.
The remaining clean reads were mapped to the Chinese Spring (T. aestivum) genome with the Burrows–Wheeler Aligner(version 0.7.17-r1188).
The MACS(version 2.2.6) program was used to identify the read-enriched regions(peaks) based on the criteria: P < 1e−10. The peaks detected from samples introduced with Halo tag only were considered as non-specific bindings, and TF peaks overlapping with peaks detected from Halo samples were removed for subsequent analysis.
Assembly: IWGSC RefSeq v1.1
Supplementary files format and content: peak files and bigwig files
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| Submission date |
Oct 11, 2022 |
| Last update date |
Oct 12, 2022 |
| 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 |
GPL25409 |
| Series (1) |
| GSE192815 |
Death and birth of transposable elements underlie subgenome convergent and divergent transcription in common wheat |
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| Relations |
| BioSample |
SAMN31239998 |
| SRA |
SRX17848227 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6628768_AP2-ERF-6A-1_rep2.sort.q20.rmdup.rpm.bw |
57.0 Mb |
(ftp)(http) |
BW |
| GSM6628768_AP2-ERF-6A-1_rep2_PE_peaks.filter.p10.bed.gz |
860.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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