|
| Status |
Public on Sep 26, 2022 |
| Title |
Sample 3_Seedlings 35S:CO biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
10 day-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 10 day-old seedlings
genotype: 35S:CO
treatment: LD ZT16
|
| Treatment protocol |
All plants were subjected to LD cycles, and samples collected at either ZT4 or ZT16.
|
| Growth protocol |
Plants were grown in controlled cabinets on peat-based compost. Seeds were previously incubated for 4 days at 4°C in the dark before sowing under LD (16 h light, 8 h dark) cycles with temperatures ranging from 22°C (day) to 18°C (night).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using E.Z.N.A.® Plant RNA Kit (Omega) from 10-day-old whole seedlings or petals following the manufacturer ́s instructions.
Libraries were prepared using 250 ng of total RNA with wit the Illumina TruSeq Stranded mRNA protocol according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The quality analysis was carried out using FASTQC.
Mapping against the reference genome TAIR10 from A. thaliana with HISAT2.
For transcript assembly and gene expression estimation in FPKM (fragments per exon kilobase and million mapped reads) the Stringtie2 software and R bioconductor package Ballgown v2.20 were used.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
May 25, 2022 |
| Last update date |
Sep 26, 2022 |
| Contact name |
Federico Valverde |
| E-mail(s) |
[email protected]
|
| Organization name |
CSIC
|
| Street address |
c/Americo Vespucio 49
|
| City |
Sevilla |
| ZIP/Postal code |
41092 |
| Country |
Spain |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE204774 |
CONSTANS and jasmonate signaling coordinate floral senescence in Arabidopsis |
|
| Relations |
| BioSample |
SAMN28656415 |
| SRA |
SRX15448562 |
