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Status |
Public on Apr 12, 2024 |
Title |
Para9150 THP-1 infection replicate 1 [Barseq13] |
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: THP-1
|
Treatment protocol |
Macrophages were infected with Ty2 and para9150 libraries for 18 hours after changing the media to high gentamycin (10 ug/mL).
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Growth protocol |
Samples were grown to OD~1 in LB, then used to infect THP-1 human macrophages at an MOI of 100. Infections were allowed to proceed for 1 hour, then cells were treated with media+high gentamycin (100 ug/mL) for 1 hour to kill extracellular bacteria. Media was then changed to low gentamycin (10 ug/mL) for the duration of the infection, which proceeded for 18 hours.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted using the epicentre masterpure dna extraction kit, which was applied to macrophages lysed with 2% saponin after the duration of the 18 hour infection. 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 |
|
|
Description |
IT010
|
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. Data was analyzed using DEseq2 analysis, as has previously been done with macrophage Tn library papers and Salmonella. Assembly: ASM754v1 for Ty2, ASM1188v1 for Para9150. Supplementary files format and content: Barseq13_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0. Supplementary files format and content: Barseq13_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
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|
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Submission date |
Mar 28, 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) |
GSE262769 |
High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq13 (Typhi and Paratyphi A infection of THP-1 human macrophages) |
GSE264519 |
High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection |
|
Relations |
BioSample |
SAMN40648991 |
SRA |
SRX24094272 |