|
| Status |
Public on Mar 14, 2019 |
| Title |
HHO2_B4Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
root protoplasts
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
organ: root
ecotype: Col-0
treatments: Nitrogen, Cycloheximide, Dexamethasone
age: 10 days
transfection: HHO2
|
| Treatment protocol |
Protoplasts were isolated from root tissue and transfected with expression vector. The following morning protoplasts were treated with 60 mM nitrogen (20 mM KNO3 + 20 mM NH4NO3), 35 uM cycloheximide and 10uM dexamethasone
|
| Growth protocol |
Arabidopsis seedlings grown on vertical plates containing MS basal media w/o C or N, 1% sucrose and 1mM KNO3
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Approximately 10,000-20,000 cells were FACS sorted into RLT buffer and frozen. Total RNA was extracted using the RNeasy Micro Kit (Qiagen) with on-column DNase treatment. mRNA was purified using Dynabeads Oligo (dT).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. Final quantity was determined using the DNA TapeStation and KAPA Library Quant qPCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were trimmed to remove low quality bases (q<10) and adapter contamination.
Gene expression levels were determined by aligning reads to the Arabidopsis thaliana genome (TAIR10) using the TopHat (v2) package and estimating read counts by the GenomicFeatures/Alignments package.
Genes responding significantly (FDR adjusted p-val <0.05) to each of the "N-early response" TFs relative to the empty vector control were identified using DESeq2 with a ~TF+Batch model.
Genome_build: TAIR10
Supplementary_files_format_and_content: Read counts output from GenomicFeatures/Alignments package
|
| |
|
| Submission date |
Jul 30, 2018 |
| Last update date |
Mar 15, 2019 |
| Contact name |
Matthew D. Brooks |
| Organization name |
USDA
|
| Department |
GCPRU
|
| Street address |
1201 W Gregory Drive
|
| City |
Urbana |
| State/province |
Illinois |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE117857 |
Genome-wide validation of the direct regulated targets for 33 nitrogen-early response transcription factors |
|
| Relations |
| BioSample |
SAMN09739314 |
| SRA |
SRX4485044 |
