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| Status |
Public on Apr 28, 2024 |
| Title |
50d_Rapeseed_seeds_RNAPII_eChIP-seq_rep2 |
| Sample type |
SRA |
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| Source name |
50d_seeds
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| Organism |
Brassica napus |
| Characteristics |
tissue: 50d_seeds
cell line: Zhongshuang 11
cell type: 50d seeds cells
chip antibody: RNAPII
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| Growth protocol |
For the collection of economically important plant organs, the plants were planted and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. For the collection of vegetativetissues, the plants were planted in greenhouses.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® sequencing (New England BioLabs, E7645) and sequenced using an Illumina Novaseq 6000 platform (paired-end 150 bp reads).
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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 |
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1
Supplementary files format and content: Narrowpeak
Supplementary files format and content: \
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| Submission date |
Sep 22, 2023 |
| Last update date |
Apr 28, 2024 |
| Contact name |
Wenying Zhong |
| E-mail(s) |
wenyingzhong@webmail.hzau.edu.cn
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| Organization name |
Huazhong Agricultural University
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| Street address |
Lion Rock Street
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| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platform ID |
GPL29911 |
| Series (2) |
| GSE243804 |
aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [ChIP-Seq] |
| GSE243806 |
aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs |
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| Relations |
| BioSample |
SAMN37513940 |
| SRA |
SRX21859140 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7795845_B4CS-101_peaks.narrowPeak.gz |
20.0 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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