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| Status |
Public on Oct 29, 2014 |
| Title |
A9430172 |
| Sample type |
SRA |
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| Source name |
maize leaf
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| Organism |
Zea mays |
| Characteristics |
genotype: SX19S10-M0120
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| Growth protocol |
B73, Mo17 and 88 Syn10 IBM DH lines were grown hydroponically, under long day conditions (16/8 hour day/night cycle at 26°C:/22°C) and harvested at 5 weeks of age
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen maize leaf tissues via Qiagen RNeasy kit for total RNA isolation (Qiagen, Valencia, California USA).
Libraries were prepared using the TruSeq paired-end mRNA-Seq kit and protocol from Illumina, Inc. and sequenced on the Illumina HiSeq 2500 system with Illumina TruSeq SBS v3 reagents. The resulting sequences were trimmed based on quality scores and mapped to the maize B73 reference genome sequence V2 and maize working gene set V5a with Tophat2.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
SX19S10-M0120
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| Data processing |
Illumina Casava software used for basecalling.
Tophat2 was used to map reads to genome and maize transcriptome (version 5a)
Cufflinks was used to discover novel transcripts
Cuffdiff was used to quantify known and novel transcripts
Genome_build: Maize transcriptome version 5a
Supplementary_files_format_and_content: Tab-delimited FPKM expression
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| Submission date |
May 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Shawn R Thatcher |
| Organization name |
University of Delaware
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| Street address |
15 Innovation Way
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19713 |
| Country |
USA |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE57337 |
Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation |
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| Relations |
| BioSample |
SAMN02746241 |
| SRA |
SRX533720 |
| 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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