|
| Status |
Public on Feb 14, 2023 |
| Title |
vil1-1 27°C RNA-seq (replicate 1) |
| Sample type |
SRA |
| |
|
| Source name |
Seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: 14 days old seedling
genotype: vil1-1
temperature: 27degreeC
|
| Treatment protocol |
Tissue (14 days old seedlinds) was harvested for experiment at ZT-6
|
| Growth protocol |
Plants were grown in long day (16-hour light, 8-hour dark) and short day (8-hour light, 16-hour dark) at 22°C or 27°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted by using TRIzol (Invitrogen) and treated with DNase I enzyme (Promega) to eliminate traces of genomic DNA
Library was prepared using NEB illumina library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
vil27
|
| Data processing |
Reads generated by Illumina NextSeq 500 platform were checked for quality using FastQC
After quality assessment, reads were aligned on TAIR10 genome using HISAT2 for RNA-seq and Bowtie2 for ChIP-seq
SAM files generated from mapping were then converted into BAM files and sorted using Samtools
For the gene counting bedtools program was used which generates raw count using BAM files
Raw count was then fed into R for differential gene expression analysis using edgeR and data visualization
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel file containing raw read count of each sample and RPKM normalized read count of each sample
Supplementary_files_format_and_content: .bw (IGV)
|
| |
|
| Submission date |
May 01, 2020 |
| Last update date |
Feb 14, 2023 |
| Contact name |
Sibum Sung |
| E-mail(s) |
sbsung@austin.utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Street address |
NMS 5.110, Stop A5000
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE149686 |
Warm temperature-triggered developmental reprogramming requires VIL1-mediated, genome-wide H3K27me3 accumulation in Arabidopsis |
|
| Relations |
| BioSample |
SAMN14789680 |
| SRA |
SRX8241072 |
