|
| Status |
Public on Nov 11, 2022 |
| Title |
seedlings, wt, rep3 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
genotype: wild type
|
| Growth protocol |
The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long day photoperiod (23°C, 16 h light/22°C, 8 h dark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (the single-ended 50-bp strategy on the BGISEQ500 platform).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads for each sample.
|
| |
|
| Submission date |
Jan 05, 2022 |
| Last update date |
Nov 11, 2022 |
| Contact name |
xinjian He |
| E-mail(s) |
hexinjian@nibs.ac.cn
|
| Organization name |
National Institute of Biological Sciences
|
| Lab |
hexinjian
|
| Street address |
No. 7, zhongguancun life science park road, changping district
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL24025 |
| Series (2) |
| GSE193095 |
Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [RNA-Seq] |
| GSE193397 |
Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility |
|
| Relations |
| BioSample |
SAMN24657155 |
| SRA |
SRX13617509 |
