|
| Status |
Public on Feb 04, 2016 |
| Title |
maize leaf R1 rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
maize leaf R1
|
| Organism |
Zea mays |
| Characteristics |
genotype: B73
developmental stage: R1
growth condition: well-watered
tissue: leaf
|
| Growth protocol |
B73 maize plants were grown in a field in Woodland, CA in 2012. Plots were designed utilizing a randomized complete block design, with four biological replicates. Drought stress was applied by withholding water after stage V8.
|
| 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).
Standard Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
A5670156
|
| 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 genome version 5a
Supplementary_files_format_and_content: Tab-delimited FPKM expression
|
| |
|
| Submission date |
Aug 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Shawn R Thatcher |
| Organization name |
University of Delaware
|
| Street address |
15 Innovation Way
|
| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19713 |
| Country |
USA |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE71723 |
Genome-wide analysis of alternative splicing during development and drought in Zea mays |
|
| Relations |
| BioSample |
SAMN03956453 |
| SRA |
SRX1132950 |
