|
| Status |
Public on Jun 01, 2020 |
| Title |
HN-elongation zone-R1 |
| Sample type |
SRA |
| |
|
| Source name |
elongation zone of leaf sixth_4nM nitrogen
|
| Organism |
Zea mays |
| Characteristics |
cultivar: maize inbred B73
tissue: the sixth Leaf
tissue compartment: elongation zone
|
| Growth protocol |
maize inbred B73 grown in hydroculture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The elongation zone of maize leaf 6 was harvested, flash frozen and stored at -80℃.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
supply 4mM nitrogen (HN)
|
| Data processing |
Raw reads were pre-processed to remove low quality regions and adapter sequences.
Clean reads from each sample were aligned to the maize reference genome (B73 RefGen_v3, http://www.maizegdb.org/assembly/) using TopHat2
Aligned reads from TopHat2 mapping were subjected to String Tie for DeNovo transcript assembly
The R package edgeR was used to identify the differentially expressed genes.The expression of each gene was normalized to fragments per kilobase of transcript per million reads (FPKM) to compare among different samples.
Genome_build: B73 RefGen_v3 (http://www.maizegdb.org/assembly/)
Supplementary_files_format_and_content: tab-delimited text files include tags,copy number and FPKM
|
| |
|
| Submission date |
Jun 02, 2017 |
| Last update date |
Jun 01, 2020 |
| Contact name |
xiaohuan mu |
| E-mail(s) |
muxiaohuan@cau.edu.cn
|
| Phone |
+8615824830720
|
| Organization name |
Henan Agricultural University
|
| Street address |
zhengzhou long zi hu
|
| City |
zheng zhou |
| ZIP/Postal code |
450002 |
| Country |
China |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE99638 |
Low-nitrogen stress reduces cell flux and cell elongation rate in maize leaf via reducing GA synthesis |
|
| Relations |
| BioSample |
SAMN07190268 |
| SRA |
SRX2881385 |
