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| Status |
Public on Mar 15, 2017 |
| Title |
dek37 |
| Sample type |
SRA |
| |
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| Source name |
kernel
|
| Organism |
Zea mays |
| Characteristics |
tissue: endosperm
age: 18 DAP
genotype: dek37
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v2 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of transcript per Million mapped reads were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensembl plants release-19 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Mar 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dawei Dai |
| E-mail(s) |
daweidai@ufl.edu
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| Organization name |
University of Florida
|
| Department |
Horticultural Sciences
|
| Street address |
2550 Hull Rd
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| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32611 |
| Country |
USA |
| |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE95769 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (WT) and dek37 mutant Transcriptomes |
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| Relations |
| BioSample |
SAMN06545436 |
| SRA |
SRX2617687 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2525640_dek37.xlsx.gz |
2.1 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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