|
| Status |
Public on Oct 05, 2022 |
| Title |
2 hour lighting rep1 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedling
growth condition: grow in dark for 7 days
light treatment: 2 hour after light treatment
genotype: wild type
|
| Treatment protocol |
etiolated seedlings were treated with light to induce de-etiolation
|
| Growth protocol |
seeds were geminated in MS medium for 7 days to induce etiolation
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen Plant RNA extraction kit (Qiagen; catalog no. 74904)
BGISEQ-500 RNA-Seq Library P reparation Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample
Raw reads were filtered by SOAPnuke software
The transcript expression level was then calculated and normalized to FPKM using RSEM software
We mapped clean reads to reference using Bowtie2\[3\], and then calculate gene expressionlevelwithRSEM
Genome_build: We use HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
|
| |
|
| Submission date |
Nov 24, 2021 |
| Last update date |
Oct 05, 2022 |
| Contact name |
Zizhen Liang |
| E-mail(s) |
zizhenliang@gmail.com
|
| Organization name |
The Chinese University of Hong Kong
|
| Street address |
The Chinese University of Hong Kong
|
| City |
Hong Kong |
| ZIP/Postal code |
NIA |
| Country |
China |
| |
|
| Platform ID |
GPL24025 |
| Series (1) |
| GSE189497 |
Transcriptomic analysis of the Arabidopsis leaf during the deetiolation |
|
| Relations |
| BioSample |
SAMN23424725 |
| SRA |
SRX13217342 |
