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Sample GSM8180475 Query DataSets for GSM8180475
Status Public on Apr 12, 2024
Title Para9150 rifampicin replicate 2 [Barseq9]
Sample type SRA
 
Source name ATCC 9150
Organism Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Characteristics tissue: ATCC 9150
genotype: Bacterial Tn library
treatment: 4 ug/mL rifampicin
Treatment protocol Each library was grown in stresses (either LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B) overnight for 16 hours.
Growth protocol Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B).
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using a Qiagen gDNA kit using standard procedures.
Purified gDNA was subjected to a barcoding PCR using Q5 polymerase, with a universal P5 primer and unique P7 for each condition, according to published protocols in Wetmore et al., 2015 mbio. This PCR only captures the barcoded region of each Tn insertion.
 
Library strategy Tn-Seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description IT042
Data processing Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: Barseq9_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq9_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq9_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: Barseq9_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.
 
Submission date Mar 29, 2024
Last update date Apr 12, 2024
Contact name Benjamin Wang
E-mail(s) bwang40@stanford.edu
Phone 9737522074
Organization name Stanford
Street address 299 Campus Drive
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Platform ID GPL34287
Series (2)
GSE262848 High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq9 (LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B)
GSE264519 High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection
Relations
BioSample SAMN40657472
SRA SRX24105039

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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