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| Status |
Public on Feb 04, 2021 |
| Title |
Flood_H3K4me3_ChIP_seq_Rep1 |
| Sample type |
SRA |
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| Source name |
Triticum aestivum 14-days-old seedlings
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| Organism |
Triticum aestivum |
| Characteristics |
tissue: 14-days-old seedlings
cultivar: Chinese Spring
chip antibody: H3K4me3
chip antibody manufacturer: Abcam
chip antibody catalog #: ab8580
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| Treatment protocol |
For hormone and NaCl treatments, germinated seeds were grown in Hoagland solution at 22 °C under long-days conditions for 7 days. The 7-day-old seedlings in Hoagland were treated with 100μm ABA, 100μm MeJA, 500μm SA and 150mM NaCl, respectively, followed by incubation for 7 days.
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| Growth protocol |
16h light, 8h dark, 22°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin or RNA was extracted from 14-days-old seedlingss, using standard protocols. 2μg total RNA (rRNA depleted) were used to prepare lncRNA-seq，2.2 μg DNA extracted from the harvested seedlings were used to prepare ChIP-seq. For DAP-seq, genomic DNA was extracted from leaves (14-days-old). 5μg gDNA was used to prepare DAP-seq library.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000/2500 system (Illumina) to produce !Sample_extract_protocol_ch1 = For DAP-seq, genomic DNA was extracted from wheat leaves using Plant DNAzol Reagent (invitrogen) and fragmented. DNA was 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405 for ChIP-seq, HISAT2 2.1.020 for RNA-seq data, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32. ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
For DAP-seq, MACS2.2.6 was used to identify protein binding sites (peaks). TF peaks which overlap with Halo peaks were removed. The top 6,000 peaks, ranked first by -log10(qvalue), then by fold enrichment, were used to discover novel DNA-binding motifs by MEME-ChIP in MEME software toolkit.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In lncRNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided. In DAP-seq, peak files were provided.
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| Submission date |
Oct 17, 2019 |
| Last update date |
Feb 04, 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 |
GPL17701 |
| Series (1) |
| GSE139019 |
An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses |
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| Relations |
| BioSample |
SAMN13048910 |
| SRA |
SRX7013460 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4126900_Flood_H3K4me3_ChIP_seq_Rep1.bw |
973.5 Mb |
(ftp)(http) |
BW |
| GSM4126900_macs_Flood_H3K4me3_Rep1_peaks.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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