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Sample GSM8218486 Query DataSets for GSM8218486
Status Public on May 01, 2024
Title ΔB11 + pCtr R2
Sample type SRA
 
Source name bacterial cultures
Organism Mycobacterium marinum
Characteristics strain: M
tissue: bacterial cultures
genotype: sRNA B11-deleted
treatment: pSMT3 control empty plasmid
Growth protocol 7H9 broth plus 10% OADC
Extracted molecule total RNA
Extraction protocol Bacterial cultures (4 mL) were mixed with 0.2 volumes of stop solution (95% ethanol and 5% phenol) and immediately frozen in liquid nitrogen. Total RNA was isolated using the Trizol method, wherein cells were resuspended in 1 mL Trizol (Invitrogen) and 0.2 mL 0.1mm Zirconium/Silica beads (Biospec) for lysis. Bacterial lysis was achieved using a Precellys 24 homogenizer (4500 rpm, 3 cycles of 30 seconds, separated by 5-minute intervals on ice). After addition of 400 μL chloroform and centrifugation in a Phase Lock Gel tube (TIANGEN Biotech) at 13,000 rpm for 15 min, 500 μL of the aqueous phase was mixed with 450 μL isopropanol and precipitated at room temperature for 30 min. The RNA pellets were then washed with 80% ethanol, dissolved in ultra-pure water (Thermo Fisher Scientific), and the RNA concentration was determined using a NanoDrop 2000 (Thermo Fisher Scientific).
Ribosomal RNAs was removed by Biotin-labeled rRNA probe. RNA was fragmented with BGI fragmentation buffer and was reverse transcribed with random hexamer. Double chain cDNA was then blunted and phosphorylated for the 5’ end, and overhang A base in the 3’ end and ligated with T-overhang adapter. After PCR application, samples were sequenced in BGISeq-500 platform
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Description sRNA B11-deleted M.marinum M strain plus pSMT3 control empty plasmid
Data processing RNA-seq was performed by BGI Group, Shenzhen, Guangdong, China. Briefly, a strand-specific cDNA library was constructed for each sample to keep the direction of RNA transcription. The obtained cDNA libraries were sequenced on an Illumina HiSeq 4000 machine.
SOAP (v2.21, -m 0 -x 1000 -s 28 -l 32 -v 5 -r 1 -p 3).The rest reads with adaptor,or with unknown bases more than 5% ,or with more than 20% low-quality bases were cleared by a software developed by BGI group. After, clear reads were mapped to reference genome with Bowtie2: v2.2.5 -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --), and expression value was caculated (http://deweylab.biostat.wisc.edu/RSEM)
Assembly: Mycobacterium marinum M strain (NC_010612.1) Chromosome (https://www.ncbi.nlm.nih.gov/nuccore/NC_010612.1) and plasmid (https://www.ncbi.nlm.nih.gov/nuccore/NC_010604.1)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
 
Submission date Apr 19, 2024
Last update date May 01, 2024
Contact name Chuan Wang
E-mail(s) chuanwang@fudan.edu.cn
Organization name Fudan University
Street address 131 # Dong An Road
City Shanghai
ZIP/Postal code 200033
Country China
 
Platform ID GPL34399
Series (1)
GSE264453 Transcriptome Profiles of Mycobacterium marinum sRNA B11-Deleted and -Completed Strains
Relations
BioSample SAMN41021558
SRA SRX24313562

Supplementary file Size Download File type/resource
GSM8218486_deltaB11_+_pCtr_R2.rtf.gz 70.3 Kb (ftp)(http) RTF
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Raw data are available in SRA

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