|
Status |
Public on Mar 22, 2024 |
Title |
at-seed-RNAseq_replicate2_Colxosd1_7DAP |
Sample type |
SRA |
|
|
Source name |
AT 7DAP Seed osd1
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: seed genotype: Col-0 x osd1
|
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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
Arabidopsis thaliana seed 7DAP of Columbia-0 crossed with osd-1 TPM.genes.crispRarf.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.
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|
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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 |
SAMN35158404 |
SRA |
SRX20419920 |