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SRX18691002: GSM6829445: 33.3_5_ale_rep1; Triticum aestivum; OTHER
1 ILLUMINA (Illumina NovaSeq 6000) run: 22.9M spots, 6.9G bases, 2.1Gb downloads

External Id: GSM6829445_r1
Submitted by: Functional Epigenomics Group, National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology,Chinese Academy of Sciences
Study: Subgenome-specific usage of transposable element-derived promoters and enhancers in bread wheat development
PRJNA814385 • SRP363290 • All experiments • All runs
show Abstracthide Abstract
Transcription start site (TSS) is the hub integrating regulatory input from promoters and enhancers. Common wheat converged three subgenomes adapted to different environment and established as a major crop worldwide. Detection of more precise and new TSS of both genes and enhancers in common wheat is the basis in interpreting transcriptional regulatory networks as well as the subgenome divergent regulation in their entirety. Overall design: In the present study, we profiled the genome wide TSS by CAGE-seq together with DNA methylation and histone modifications from four typical tissues in common wheat, the resulting catalogue of enhancers enabled more precise detection of ubiquitous and tissue specific TSS usage of coding genes and enhancers.
Sample: 33.3_5_ale_rep1
SAMN32224706 • SRS16133743 • All experiments • All runs
Organism: Triticum aestivum
Library:
Name: GSM6829445
Instrument: Illumina NovaSeq 6000
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: Total genomic DNA was extracted from the tissue to generate the ALE-seq library. The first step was to connect an adapter containing the T7 promoter sequence to the end of 5' end of the eclDNA, followed by in vitro transcription using T7 RNA polymerase. Reverse transcription was then performed using a primer that binds to the transcript of the PBS region, and LTR-RTs showing transposition potential were extracted.
Runs: 1 run, 22.9M spots, 6.9G bases, 2.1Gb
Run# of Spots# of BasesSizePublished
SRR2272948022,943,5776.9G2.1Gb2023-10-12

ID:
25756287

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