|
| Status |
Public on Oct 01, 2021 |
| Title |
RS-A/RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Flower buds
|
| Organism |
Brassica napus |
| Characteristics |
strain: Pactol
tissue: Flower buds
phenotype: Restored
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from 1/10th of the lysates used for Ribo-Seq analysis (see GEO Submission (GSE178543)) and treated with the Ribo-Zero rRNA Removal Kit (Illumina). One hundred ng of the rRNA-depleted RNAs were used for library construction using the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific) according the manufacturer’s instructions. Next generation sequencing was performed on a NextSeq 500 sequencer (single end, 75 nt).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. After cytosolic, plastid and mitochondrial rRNA removal, reads comprised between 20-65 nucleotides were selected for mapping to the rapeseed mitochondrial genome using Bowtie 2 with default parameters but allowing 1 missmatch.
Genome_build: Brassica napus mitochondrial DNA (GenBank: AP006444.1) to which we manually added the orf138 gene.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 23, 2021 |
| Last update date |
Oct 01, 2021 |
| Contact name |
HAKIM MIREAU |
| E-mail(s) |
[email protected]
|
| Organization name |
INRAE
|
| Lab |
INSTITUT JEAN-PIERRE BOURGIN
|
| Street address |
Route de Saint-Cyr
|
| City |
Versailles |
| ZIP/Postal code |
F-78000 |
| Country |
France |
| |
|
| Platform ID |
GPL25850 |
| Series (1) |
| GSE178722 |
The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA [RNA-seq] |
|
| Relations |
| BioSample |
SAMN19835104 |
| SRA |
SRX11204259 |
