|
| Status |
Public on May 04, 2021 |
| Title |
dek3-2_r2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: dek3-2 mutant
age: 7 days old
tissue: whole seedling
|
| Growth protocol |
For seed germination, seeds were sterilized and then stratified for 3 days at 4 ℃ under dark condition; seeds were germinated on 1/2 Murashige and Skoog (MS) plates containing 0.8% Phytagel. Seedlings were grown in growth chamber with 16-h light/8-h dark cycles at 22℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolaed from 7-day-old seedlings using Purelink Plant RNA Regent (Invitrogen) according to manufacturer's instructions.
RNA-Seq libraries were prepared by NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (E7420) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads wer mapped to the TAIR10 Arabidopsis genome using HISAT2 with default parameters
Featurecount was used to count read numbers of each gene
edgeR was used to identify differentially expressed genes
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of each gene for each sample
|
| |
|
| Submission date |
Dec 23, 2020 |
| Last update date |
May 04, 2021 |
| Contact name |
Wei Zong |
| E-mail(s) |
weiz@austin.utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
NMS 5.268, Stop A5000
|
| City |
Austin |
| State/province |
Texas |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE163742 |
RNA-Seq of Col-0, dek3-2, dek4-2, and dek3-2 dek4-2 (dd-2) 7-day-old seedlings in Arabidopsis |
|
| Relations |
| BioSample |
SAMN17142420 |
| SRA |
SRX9721559 |
