|
| Status |
Public on Apr 12, 2024 |
| Title |
Para time 0 replicate 2 [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: none
|
| Treatment protocol |
Macrophages were infected with Ty2 and para9150 libraries for 18 hours after changing the media to high gentamycin (10 ug/mL).
|
| 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.
|
| |
|
| Library strategy |
Tn-Seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
time0 is used as reference for other samples
|
| 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.
|
| |
|
| 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 |
SAMN40648993 |
| SRA |
SRX24094270 |
