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| Status |
Public on Apr 12, 2024 |
| Title |
Para9150 rifampicin replicate 2 [Barseq9] |
| 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: 4 ug/mL rifampicin
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| Treatment protocol |
Each library was grown in stresses (either LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B) 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 LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B).
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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 |
IT042
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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: 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.
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| Submission date |
Mar 29, 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) |
| 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 |
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| Relations |
| BioSample |
SAMN40657472 |
| SRA |
SRX24105039 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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