|
| Status |
Public on Nov 11, 2021 |
| Title |
WT_SPI2inducing |
| Sample type |
SRA |
| |
|
| Source name |
Salmonella enterica sero. Typhimurium (14028s)
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
genotype: WT
growth_conditions: SPI-2 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 |
SAMN22164183 |
| SRA |
SRX12529246 |
