|
| Status |
Public on Mar 08, 2023 |
| Title |
psesd_aCcr1_2 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Sulfolobus islandicus |
| Characteristics |
tissue: cells
cell line: strain
cell type: strain
genotype: aCcr1 overexpressed strain
treatment: Arabinose induction
|
| Treatment protocol |
For transcriptomic analysis, culture was inoculated with an initial OD600 of 0.05. The cells were pelleted at 6,000 g for 10 min after 12 h of cultivation when the OD600 reached approximately 0.2. The pellet was resuspended in 1 ml PBS buffer. The cells were pelleted again and stored at -80°C.
|
| Growth protocol |
Strains of Sis/pSeSD and Sis/pSeSD-aCcr1 were cultured in ATV medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
aCcr1 overexpressed
|
| Data processing |
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: REY15A
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Nov 25, 2022 |
| Last update date |
Mar 08, 2023 |
| Contact name |
yunfeng Yang |
| E-mail(s) |
[email protected]
|
| Phone |
18382465184
|
| Organization name |
Shandong University
|
| Street address |
72 Binhaidadao, Aoshanwei, Jimo
|
| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266237 |
| Country |
China |
| |
|
| Platform ID |
GPL32733 |
| Series (2) |
| GSE218792 |
A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea [RNA-seq] |
| GSE218793 |
A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea |
|
| Relations |
| BioSample |
SAMN31873517 |
| SRA |
SRX18379168 |
