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| Status |
Public on May 09, 2020 |
| Title |
RTseq_6 |
| Sample type |
SRA |
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| Source name |
RT-PCR
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| Organism |
Zea mays |
| Characteristics |
tissue: shoot
genotype: B73/Mo17 F1 hybrid
age: 6-day-old seedlings
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
amplicon-PCR and RT-PCR was perfromed followed by a regular culumn-purification step.
Libraries were prepared using an mRNA preparation kit (Illumina) following a standard protocol (https://www.purdue.edu/hla/sites/genomics/wi-deseq-2/)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and processed follow the Museq pipeline for TSD identification. Please refer to the following method paper for details: Cost-Effective Profiling of Mutator Transposon Insertions in Maize by Next-Generation Sequencing. Xinyan Zhang, Meixia Zhao and Damon Lisch. Methods in Molecular Biology, 2020, 2072: 39-50.).
For RT-PCR-based quantification of allele frequency, paired SNP-containing sequenced tags were searched against the fastq files for each samples.
Genome_build: AGPv4 B73
Supplementary_files_format_and_content: tab-delimited text files include TSD-coordinates and allele frequency of their nearby genes (counts of reads representing the expression products of either B73 or Mo17 copy in the hybrid plants)
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| Submission date |
Mar 09, 2020 |
| Last update date |
May 09, 2020 |
| Contact name |
Damon Lisch |
| Organization name |
Purdue University
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| Street address |
915 West State Street
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platform ID |
GPL19255 |
| Series (1) |
| GSE146647 |
Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes |
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| Relations |
| BioSample |
SAMN14337482 |
| SRA |
SRX7879081 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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