|
| Status |
Public on May 07, 2019 |
| Title |
At1+_3-2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
developmental stage: 10 day old seedlings
background strain: Col-0
genotype: AtIPCS1 over expressing line
treatment: untreated
|
| Treatment protocol |
Seedling were untreated
|
| Growth protocol |
Arabidopsis thaliana plants were grown on 0.8% Murashige and Skoog (MS) agar for 10 days. Plants were grown at 20°C under 16h day/8 h night photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the ReliaPrep™ RNA Tissue Miniprep System (Promega) and processed as per manufacturer’s instructions.
Libraries were prepared using the Illumina Truseq stranded mRNA sample preparation kit, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastq files were aligned to Arabidopsis genome (Arabidopsis Araport 2017) using STAR
BAM files resulting from the alignments were summarized to genes using the HTSeq package
Expression data was normalized using the DESeq package from bioconductor in R
Differentially expressed genes (³2-fold and £5% false discovery rate) were identified using the DESeq package
Genome_build: Arabidopsis thaliana genome (Arabidopsis Araport 2017)
Supplementary_files_format_and_content: Tab-delimited text files include log2 counts per million (CPM) values for each sample
|
| |
|
| Submission date |
Mar 28, 2019 |
| Last update date |
May 07, 2019 |
| Contact name |
Paul William Denny |
| E-mail(s) |
p.w.denny@durham.ac.uk
|
| Phone |
01913343983
|
| Organization name |
Durham University
|
| Department |
Biosciences
|
| Street address |
Lower Mountjoy
|
| City |
Durham |
| State/province |
Durham |
| ZIP/Postal code |
DH1 3LE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE129016 |
Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN11282549 |
| SRA |
SRX5590282 |
