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Sample GSM5965331 Query DataSets for GSM5965331
Status Public on Aug 03, 2022
Title tmRNA reverse mutant rep1
Sample type SRA
 
Source name Bacteria
Organism Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10
Characteristics cell type: biofilm and planktonic bacteria
strain: revertant strain (MB)
genotype: SsrA-
Extracted molecule total RNA
Extraction protocol The growth status of samples in LBMG medium were analyzed and 36 hours was selected. The cells at the selected time point were collected and total RNA was extracted using the Total RNA Kit (OMEGA).
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 Bacillus subtilis NCIB 3610
Data processing Illumina Casava1.7 software used for base-calling.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: CP020102
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
 
Submission date Mar 22, 2022
Last update date Aug 03, 2022
Contact name Shanshan Xu
E-mail(s) xusslzz@szu.edu.cn
Organization name Shenzhen University
Street address Xueyuan Avenue, No. 1066
City Shenzhen
ZIP/Postal code 518000
Country China
 
Platform ID GPL32075
Series (1)
GSE199151 Transcriptome sequencing data analysis of Bacillus subtilis NCIB 3610 wild-type strain, tmRNA mutant strain and MB revertant strain
Relations
BioSample SAMN26870592
SRA SRX14564824

Supplementary file Size Download File type/resource
GSM5965331_MB-1.txt.gz 37.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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