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| Status |
Public on Jan 31, 2023 |
| Title |
Spirosoma montanitarrae DY10T, UVC, 12 hr |
| Sample type |
SRA |
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| Source name |
12 hr
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| Organism |
Spirosoma montaniterrae |
| Characteristics |
strain: DY10T
cell type: 12 hr
treatment: UVC
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| Treatment protocol |
For the UVC treatment, the early stationary phase cells on TGY agar plates were exposed to 600 JM-2 of ultraviolet using an ultraviolet crosslinker (UVP, CX-2000, CA, USA) at 254nm.
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| Growth protocol |
The bacterial strain DY10T (KCTC 23999T) was grown at 25ºC in liquid nutrient-rich medium tryptone glucose yeast extract (TGY; 1% tryptone, 0.1% glucose and 0.5% yeast extract) or TGY agar plates.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The post-radiation cells of UVC were collected by centrifugation (17,500 × g for 5 min) at 5min, 1hr, 3hr and 12hr with washing and stored with RNAlater solution at -80ºC. Total RNA was isolated using the Ambion Ribopure-Yeast RNA kit, according to manufacturer's instructions.
Strand-specific RNA-seq library preparation and sequencing was carried out as a paid service by Somagenics Inc., Santa Cruz, California, USA. Paired-end reads (Illumina NextSeq 500 v2, 2 × 150 bp, 3 Gb average output per sample) were obtained from strain DY10T.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
12hr
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| Data processing |
Reads of each samples’ adaptor trimmed by Trim galore (version 0.6.7) for quality control.
Clean reads of the samples were aligned against the reference genome (Build: ASM198895v1) using Hisat2 (version 2.1.0).
HTSeq (version 0.12.4) was used to quantify the mapped reads per ORF.
Assembly: ASM198895v1
Supplementary files format and content: comma-delimited text files include read counts values for each Sample. The data consists of 6 columns, the first column represents the gene locus ID on the reference genome, and the 2nd to 6th columns represent the read counts obtained from each sample.
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| Submission date |
Jan 24, 2023 |
| Last update date |
Jan 31, 2023 |
| Contact name |
Changyun Cho |
| E-mail(s) |
joebrother@snu.ac.kr
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| Organization name |
Seoul National University
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| Street address |
1, Gwanak-ro, Gwanak-gu
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| City |
seoul |
| State/province |
Not US or Canada |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platform ID |
GPL33055 |
| Series (1) |
| GSE223604 |
Characterization of radiation‑resistance mechanism in Spirosoma montaniterrae DY10T in terms of transcriptional regulatory system |
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| Relations |
| BioSample |
SAMN32887536 |
| SRA |
SRX19148619 |
| 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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