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Sample GSM5618845 Query DataSets for GSM5618845
Status Public on Nov 11, 2021
Title ∆dam_SPI1inducing
Sample type SRA
 
Source name ∆dam Salmonella enterica sero. Typhimurium (14028s)
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics genotype: delta-dam
growth_conditions: SPI-1 inducing conditions
Growth protocol For SPI-1 inducing conditions, bacteria were grown overnight at 37C in LB broth and subcultured 1:33 into LB broth before growth for 2 hours and 40 minutes. For SPI-2 inducing conditons, bacteria were grown overnight at 37C in LB broth and subcultured 1:50 in LPM media (see Coombes et al. 2004) for 4 hours.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using a Dneasy Blood and Tissue Kit. The optional RNase step was performed.
Multiplexed SMRTbell libraries for sequencing on the PacBio Sequel system were prepare from 1 μg of each microbial gDNA sample. Shearing of gDNA was performed using g-TUBE and centrifugation at 2029 x g for 2 minutes to achieve a target mode size of 10 kb - 15 kb.SMRTbell libraries were then prepared using the SMRTbell® Express Template Prep Kit 2.0. Two pools of 8 indexed libraries were prepared. Each pool was then sequenced on a PacBio Sequel SMRTcell using sequencing chemistry 3.0 and 10 hour movie length.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Sequel
 
Data processing Library strategy: Single-molecule real-time (SMRT) sequencing
m6A methylation calls were performed using the pbsmrtpipe base modification and motif detection pipeline (Smrtlink v7.0.1.66975 ) with Salmonella enterica serovar Typhimurium strain 14028s (ASM2216v1) as the reference genome . For sites at or above 50x coverage, sites with a phred-based quality score greater than 40 were marked as “1”, for strong evidence of methylation; sites with >=50x coverage but below QV40 were marked as “0” for unlikely to be methylated. For sites below 50x coverage, methylation status was not estimated. Assigning methylated bases to motif(s) was performed by comparing the context of the base to known or identified motifs using Microsoft Excel.
Genome_build: Salmonella enterica serovar Typhimurium strain 14028s (ASM2216v1)
Supplementary_files_format_and_content: WT_MetJ_Dam_ProcessedSMRTseq.xlsx
 
Submission date Oct 08, 2021
Last update date Nov 11, 2021
Contact name Jeffrey Bourgeois
E-mail(s) Jeffrey.Bourgeois@tufts.edu
Organization name Tufts University
Street address 136 Harrison Ave
City Boston
ZIP/Postal code 02111
Country USA
 
Platform ID GPL30825
Series (2)
GSE185077 Whole-genome integration of DNA methylomics and transcriptomics in Salmonella enterica sero. Typhimurium (14028s)
GSE185578 PacBio SMRT-seq of wild-type, ∆metJ, and ∆dam Salmonella enterica serovar Typhimurium (14028s)
Relations
BioSample SAMN22164185
SRA SRX12529244

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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