|
| Status |
Public on Dec 15, 2024 |
| Title |
RNA_Tko_scpB_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
KOD1
|
| Organism |
Thermococcus kodakarensis |
| Characteristics |
cell line: KOD1
genotype: scpB deletion
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were grown to mid-to-late log phase and used for RNA extraction. 23S, 16S, and 5S rRNAs were removed using complementary DNA oligos and Rnase H.
Libraries were constructed NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were counted using Salmon version 1.9.0 (Patro et al., 2017). Differentially expressed genes were identified using edgeR version 3.40.2 (Robinson et al., 2010).
Assembly: GCA_000009965.1
Supplementary files format and content: Tab-delimited tables showing Transcripts Per Million (TPM) values for each gene.
|
| |
|
| Submission date |
May 13, 2024 |
| Last update date |
Dec 15, 2024 |
| Contact name |
Naomichi Takemata |
| Organization name |
Kyoto University
|
| Department |
Synthetic Chemistry and Biological Chemistry
|
| Street address |
Kyoto University, Katsura, Nishikyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
615-8510 |
| Country |
Japan |
| |
|
| Platform ID |
GPL28196 |
| Series (1) |
| GSE267299 |
Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [RNA-seq] |
|
| Relations |
| BioSample |
SAMN41382072 |
| SRA |
SRX24534877 |
