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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 12, 2023 |
| Title |
33.3_6_ale_rep1 |
| Sample type |
SRA |
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| Source name |
spikelets
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| Organism |
Triticum aestivum |
| Characteristics |
cultivar: Fielder
tissue: spikelets
genotype: POL IV mutant
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| Extracted molecule |
genomic DNA |
| Extraction 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For ALE-seq data,The sequencing reads were trimmed with the cutadapt , and clean reads were aligned to the IWGSC reference sequence (version 1.0) with Bowtie2(version 2.3.5) . IGV was used to visualize the sequencing data. For the alignment-based approach, the for-ward and reverse reads were merged to yield the full-length fragment sequences and statistic the coverage in the long terminal region of LTR retrotransposon. Only the full-length fragment started from the 5’ of the long terminal region is counted.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: bigwig file for each ALE-seq sample
Library strategy: ALE-seq
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| Submission date |
Dec 14, 2022 |
| Last update date |
Oct 12, 2023 |
| 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) |
| GSE198284 |
Subgenome-specific usage of transposable element-derived promoters and enhancers in bread wheat development |
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| Relations |
| BioSample |
SAMN32224705 |
| SRA |
SRX18691003 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6829446_33.3_6_ale_rep1.rmmul.bw |
136.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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