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Status |
Public on Apr 12, 2024 |
Title |
Para InSPI2, rep 1 |
Sample type |
SRA |
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Source name |
ATCC 9150
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Organism |
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 |
Characteristics |
tissue: ATCC 9150 genotype: Bacterial Tn library treatment: InSPI2
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Treatment protocol |
Each library was grown in a different minimal media (NonSPI2, InSPI2, InSPI2-MG, M9 glucose) overnight for 16 hours
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Growth protocol |
Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either NonSPI2, InSPI2, inSPI2-Mg, or M9 glucose)
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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.
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Library strategy |
Tn-Seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 4000 |
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Description |
IT011 Barseq1_Para9150_processed.csv
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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: Barseq1_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0 Supplementary files format and content: Barseq1_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0 Supplementary files format and content: Barseq1_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0 Supplementary files format and content: Barseq1_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0
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Submission date |
Mar 08, 2024 |
Last update date |
Apr 12, 2024 |
Contact name |
Benjamin Wang |
E-mail(s) |
bwang40@stanford.edu
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Phone |
9737522074
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Organization name |
Stanford
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Street address |
299 Campus Drive
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City |
Palo Alto |
State/province |
CA |
ZIP/Postal code |
94304 |
Country |
USA |
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Platform ID |
GPL34287 |
Series (2) |
GSE261214 |
High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq1 (NonSPI2, InSPI2, InSPI2Mg, M9glucose) |
GSE264519 |
High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection |
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Relations |
BioSample |
SAMN40341474 |
SRA |
SRX23885381 |
Supplementary data files not provided |
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Raw data are available in SRA |
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