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| Status |
Public on Oct 15, 2014 |
| Title |
wild type |
| Sample type |
SRA |
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| Source name |
kernel
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| Organism |
Zea mays |
| Characteristics |
tissue: endosperm
age: 15 DAP
genotype/variation: wild type
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| 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
Fragments Per Kilobase of exon per Megabase of library size (FPKM) 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: B73 RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Sep 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Weiwei Qi |
| E-mail(s) |
weiweiqi@shu.edu.cn
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| Organization name |
Shanghai University
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| Street address |
333 Nanchen Road
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| City |
Shanghai |
| ZIP/Postal code |
200444 |
| Country |
China |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE61830 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and opaque2 mutant Transcriptomes |
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| Relations |
| BioSample |
SAMN03083483 |
| SRA |
SRX712854 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1515455_WT.txt.gz |
587.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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