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Sample GSM7445649 Query DataSets for GSM7445649
Status Public on Jun 07, 2023
Title BXD9.TyJ_rep1
Sample type SRA
Source name homogenized mouse spleen
Organism Mycobacterium tuberculosis H37Rv
Characteristics h37rv genotype: himar1 transposon library
mouse strain: BXD9.TyJ
infection length (days): 28
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.
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.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Description CSmith_TraCS075
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 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
Submission date Jun 05, 2023
Last update date Jun 07, 2023
Contact name Clare Smith
Organization name Duke University
Department MGM
Lab Smith Lab
Street address 207 Research Drive
City Durham
State/province North Carolina
ZIP/Postal code 27710
Country USA
Platform ID GPL20677
Series (1)
GSE234093 Genome-wide host loci regulate M. tuberculosis fitness in immunodivergent mice.
BioSample SAMN35621889
SRA SRX20592505

Supplementary file Size Download File type/resource
GSM7445649_BXD9.TyJ_rep1_raw_templates.txt.gz 277.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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