|
| Status |
Public on May 15, 2019 |
| Title |
IE Rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: Samsun
tissue: leaves
age: 7 weeks since seeding
isoprene emission phenotype: Isoprene emitting
|
| Treatment protocol |
NE does not emit isoprene; IE emits isoprene
|
| Growth protocol |
Plants were grown on Sure-Mix growing medium in greenhouses
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany)
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA) following the manufacturer's recommendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing reads were cleaned and trimmed using Trimmomatic version 0.32 (Bolger et al., 2014)
Cleaned reads were examined with FASTQC (Andrews, 2012) for quality control
Reads were mapped to the reference genomes, Nicotiana tabacum (TN90) and Arbidopsis thaliana (TAIR10)
To calculate read counts for each gene, Rsubread version 3 (Liao et al., 2013) tool (featureCounts function) was used to build read count matrix.
Read count matrix was analyzed using the linear-model based Limma::Voom package (Law et al., 2014) to calculate the gene expression values (RPKM) and perform gene DE statistical analyses
Genome_build: TAIR10 and TN90. Please see the gff3 file on the series record with Nicotiana tabacum gene coordinates.
Supplementary_files_format_and_content: Excel files include RPKM values for each sample
|
| |
|
| Submission date |
Oct 23, 2018 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Sharkey |
| E-mail(s) |
tsharkey@msu.edu
|
| Phone |
(517) 353-3257
|
| Organization name |
Michigan State University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
MSU-DOE Plant Research Laboratory
|
| Street address |
612 Wilson Rd, Rm 210 Plant Biology Building
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL22345 |
| Series (2) |
| GSE121675 |
Alterations in Gene Expression in Nicotiana tabacum Expressing ISPS |
| GSE121676 |
Alterations in Gene Expression in Arabidopsis thaliana and Nicotiana tabacum Expressing ISPS |
|
| Relations |
| BioSample |
SAMN10280978 |
| SRA |
SRX4923784 |
