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| Status |
Public on Apr 12, 2024 |
| Title |
mv D23580 Nitric oxide replicate 1 [Barseq4] |
| Sample type |
SRA |
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| Source name |
D23580
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| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. D23580 |
| Characteristics |
tissue: D23580
genotype: Bacterial Tn library
treatment: 1 mM spermine NONOate
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| Treatment protocol |
Each library was grown in stresses (either InSPI2 stress, H2O2, nitric oxide, sodium hypochlorite) 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 InSPI2 stress, H2O2, nitric oxide, sodium hypochlorite).
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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 |
IT016
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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: barseq4_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: barseq4_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: barseq4_para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: barseq4_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.
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| Submission date |
Mar 18, 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
|
| 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 |
GPL34288 |
| Series (2) |
| GSE261860 |
High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq4 (InSPI2, hydrogen peroxide (H2O2), nitric oxide (NO), sodium hypochlorite (bleach)) |
| GSE264519 |
High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection |
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| Relations |
| BioSample |
SAMN40533152 |
| SRA |
SRX23985241 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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