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| Status |
Public on Jun 20, 2023 |
| Title |
E233S, biol rep 3 |
| Sample type |
SRA |
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| Source name |
microbial cells
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| Organism |
Sulfolobus islandicus |
| Characteristics |
tissue: microbial cells
strain: REY15A
cell type: microbial cells
genotype: WT
treatment: no treatment
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| Treatment protocol |
Cultures were treated with 3 μM NQO when their OD(600nm) reached 0.2.
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| Growth protocol |
S. islandicus strains were grown in MTSUV medium (Basic mineral medium+Typtone+Sucrose+Uracil+Vatamin) at 75 oC.
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
The wild type strain E233S mock-treated for 6 h, biol rep 3
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| Data processing |
Illumina Casava 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the whole genome of S. islandicus REY15A (Guo, et al., 2011) 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.
Assembly: REY15A
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Oct 08, 2022 |
| Last update date |
Jun 20, 2023 |
| Contact name |
Qihong Huang |
| E-mail(s) |
huangqihong@sdu.edu.cn
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| Phone |
15063382551
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| Organization name |
Shandong University
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| Street address |
72 Binhaidadao, Aoshanwei, Jimo
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| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266237 |
| Country |
China |
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| Platform ID |
GPL32733 |
| Series (1) |
| GSE215078 |
Effect of deletion of Sisfha on gene expression of Saccharolobus islandicus REY15A in the presence of 4-nitroquinoline 1-oxide (NQO) |
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| Relations |
| BioSample |
SAMN31215615 |
| SRA |
SRX17833778 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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