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Sample GSM6965272 Query DataSets for GSM6965272
Status Public on Jan 31, 2023
Title Spirosoma montanitarrae DY10T, UVC, 1 hr
Sample type SRA
 
Source name 1 hr
Organism Spirosoma montaniterrae
Characteristics strain: DY10T
cell type: 1 hr
treatment: UVC
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.
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 1hr
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.
 
Submission date Jan 24, 2023
Last update date Jan 31, 2023
Contact name Changyun Cho
E-mail(s) joebrother@snu.ac.kr
Organization name Seoul National University
Street address 1, Gwanak-ro, Gwanak-gu
City seoul
State/province Not US or Canada
ZIP/Postal code 08826
Country South Korea
 
Platform ID GPL33055
Series (1)
GSE223604 Characterization of radiation‑resistance mechanism in Spirosoma montaniterrae DY10T in terms of transcriptional regulatory system
Relations
BioSample SAMN32887538
SRA SRX19148617

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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