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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 07, 2023 |
| Title |
BXD29.Ty_rep1 |
| Sample type |
SRA |
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| Source name |
homogenized mouse spleen
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| Organism |
Mycobacterium tuberculosis H37Rv |
| Characteristics |
h37rv genotype: himar1 transposon library
mouse strain: BXD29.Ty
infection length (days): 28
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| Treatment protocol |
Mice were infected with 1.0E+06 CFU of saturated Himar1 transposon mutants delivered via intravenous tail vein injection. At 4 weeks post-infection, mice were euthanized and organs harvested.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Spleens from infected mice were homogenized and approximately 1.0E+06 CFU per mouse was plated on 7H10 agar with 20ug/mL kanamycin. After three weeks of growth, colonies were harvested by scraping, and genomic DNA was extracted as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling, Methods Mol Biol: 1279:79-95.
Libraries were prepared for Illumina sequencing using custom primers as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 1279:79-95. In the majority of cases, two replicate mouse libraries were used per genotype. Only a single TnSeq library was obtained for BXD48a and BXD51. Five replicate libraries were obtained for in vitro-grown libraries.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
CSmith_TraCS276
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| Data processing |
Basecalls performed using CASAVA version 1.8
100-base paired-end reads were trimmed and aligned to the M. tuberculosis H37Rv genome to identify sites of himar1 insertion. Custom Perl programs available at https://github.com/sassettilab/Bellerose_et_al_mSystems_TnSeq_analyses were used for the read trimming and subsequently to summarize insertion counts at each genomic TA dinucleotide (see subdirectory 'TnSeq_insertion_counts_v6' under the aforementioned Github link).
Insertion mutant counts across all libraries were normalized by beta-geometric correction (DeJesus, M.A., Ambadipudi, C., Baker, R., Sassetti, C., and Ioerger, T.R. (2015). TRANSIT--A Software Tool for Himar1 TnSeq Analysis. PLoS Comput Biol: 11, e1004401), binned by gene, and replicate values for each mouse genotype averaged.
Assembly: NC_018143.2
Supplementary files format and content: Tab-delimited text files generated in the custom data processing pipeline: col 1, genome coordinate; col 2, unique insertion counts
Library strategy: TnSeq
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| Submission date |
Jun 05, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Clare Smith |
| E-mail(s) |
clare.m.smith@duke.edu
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| Organization name |
Duke University
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| Department |
MGM
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| Lab |
Smith Lab
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| Street address |
207 Research Drive
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| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
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| Platform ID |
GPL20677 |
| Series (1) |
| GSE234093 |
Genome-wide host loci regulate M. tuberculosis fitness in immunodivergent mice. |
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| Relations |
| BioSample |
SAMN35621887 |
| SRA |
SRX20592507 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7445651_BXD29.Ty_rep1_raw_templates.txt.gz |
271.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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