|
| Status |
Public on Mar 22, 2024 |
| Title |
at-seed_RNAseq_replicate2_Col_4DAP |
| Sample type |
SRA |
| |
|
| Source name |
AT 4DAP Seed Col
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seed
genotype: Col-0
|
| Treatment protocol |
Anthers were removed from the flowers two days before hand-pollination. Resulting siliques were opened at 4- or 7-DAP and seeds were carefully removed in RNAlater solution.
|
| Growth protocol |
Seeds were sown on plates containing Murashige and Skoog medium and stratified at 4°C for two days. The plates were transferred to a growth chamber for two weeks (16 h light/8 h dark; 60µmol/s/m²; 22°C). Seedlings were pricked onto soil and grown in phytotron chambers (16 h light/8 h dark; 150µmol/s/m²; 21°C; 70% humidity).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the plant RNeasy Kit from Qiagen. Total RNA was treated with DNAseI. mRNAs were specifically isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module from NEB (E7490S). The libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S).
Library construction and sequencing were performed at Novogene on an Illumina Novaseq platform in paired-end mode and with 150bp read length.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Arabidopsis thaliana seed 4DAP of Columbia-0
TPM.genes.arf22.txt
|
| Data processing |
Reads were trimmed by removing the 5 bp from the 5’ end and 20 bp from the 3' end and mapped in a paired-end mode to the Arabidopsis (TAIR10) genome using using hisat2. Gene expression levels (TPM-transcript per million) were calculated using stringtie.
Assembly: TAIR10
Supplementary files format and content: RNA-seq: expression levels (TPM-transcript per million) are shown for genes in TAIR10 for each condition and replicate.
|
| |
|
| Submission date |
May 18, 2023 |
| Last update date |
Mar 22, 2024 |
| Contact name |
Juan C Santos-González |
| E-mail(s) |
juan.santos@slu.se
|
| Organization name |
SLU
|
| Department |
Department of Plant Biology and Forest Genetics
|
| Lab |
Köhler's lab
|
| Street address |
Almas Allé 5
|
| City |
Uppsala |
| State/province |
Uppsala |
| ZIP/Postal code |
75007 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE232803 |
Parental conflict driven regulation of endosperm cellularization by a family of Auxin Response Factors |
|
| Relations |
| BioSample |
SAMN35158392 |
| SRA |
SRX20419932 |
