|
| Status |
Public on Nov 08, 2023 |
| Title |
root-N_mRNA, Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: M82
tissue: root
treatment: -N
|
| Treatment protocol |
Twenty-two day old plants were transferred to nitrogen free media for four days and then either replenished with fresh nitrogen free media (-N condition) or resupply of media containing nitrate (+N condition). After 6 hours of treatment, -N and +N samples were harvested.
|
| Growth protocol |
Plants were germinated on 1/2 strength MS plates and then transferred to a hydroponic system under greenhouse conditions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tomato root and shoot tissue was ground in liquid nitrogen and total RNA was extracted using mirVana kit following the manufacturer’s protocol for total RNA extraction. Turbo DNase was used to remove contaminating DNA and then the quality of extract total RNA was analyzed using Bioanalyzer in Purdue Genomics Core.
Poly(A) RNA was prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
raw_counts.txt
|
| Data processing |
ChIP-Seq data was trimmed using CutAdapt and aligned using Bowtie2. Paired reads were converted to fragments and dynamic islands were called using SICER-df.
RNA-Seq data was trimmed using CutAdapt and aligned using TopHat2. The gene counts were generated from mapped reads using htseq and counts were normalized with EDAseq, while differentially expressed genes were determined using DESeq2.
Genome_build: SL4.0
Supplementary_files_format_and_content: raw_counts.txt, SICER-df output files
|
| |
|
| Submission date |
Feb 16, 2022 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Ryan Patrick |
| Organization name |
Purdue University
|
| Street address |
625 Agriculture Mall Dr
|
| City |
West Lafayette |
| State/province |
Indiana |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL27957 |
| Series (1) |
| GSE196887 |
Histone code dynamics during nitrogen response in tomato |
|
| Relations |
| BioSample |
SAMN25997904 |
| SRA |
SRX14204942 |
