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| Status |
Public on Nov 30, 2020 |
| Title |
AK58_leaf_HiC_rep2 |
| Sample type |
SRA |
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| Source name |
AK58
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| Organism |
Triticum aestivum |
| Characteristics |
tissue: leaf
cultivar: AK58
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| Treatment protocol |
No treatment applied
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| Growth protocol |
Seeds were germinated and cultured with water in Petri dishes for 1 week, then transferred into nutrient solution cultured for another 2 weeks till three-leaf stage, in a growth chamber with 20 °C/18 °C (day/night), 16 h/8 h (light/dark). Leaves were harvested at 11:00 AM-12:00 PM
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bisulfite and RNA sequencing samples were prepared with 2.2 μg DNA and 2μg total RNA (rRNA depleted) extracted from the harvested leaves respectively.
The library were constructed and the subsequent deep sequencing was completed by Novogene Co Ltd. For in situ HiC library, rep1 used HindIII enzyme and rep2 used DpnII enzyme.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Sequencing reads were cleaned with the Trim Galore (version 0.4.4), Trimmomatic (version 0.36) , and Sickle programs, which eliminated bases with low-quality scores (< 25), irregular GC contents, sequencing adapters, and short reads.
The cleaned reads were mapped to AK58 genome using Bismark_v0.19.0 for bisulfite-sequencing data, HISAT2(v2.1.0)for RNA-sequencing data, HiC-Pro(v2.11.1) for HiC-sequencing data.For smRNA-seq, cleaned reads of 24-nt were mapped to AK58 genome using Shortstack(v3.8.5)
Genome_build: AK58 genome
Supplementary_files_format_and_content: In RNA-seq, read counts for genes were provided;In smRNA-seq ,24nt-sRNA cluster files were provided; In Bisulfite-seq ,tdf files with position and methylation ratio were provided.
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| Submission date |
Jun 17, 2020 |
| Last update date |
Dec 04, 2020 |
| 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 |
GPL24354 |
| Series (1) |
| GSE139020 |
Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression |
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| Relations |
| BioSample |
SAMN15297854 |
| SRA |
SRX8565924 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4623385_AK58_leaf_HiC_rep2_allValidPairs.txt.gz |
3.4 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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