|Public on Dec 01, 2023
|patient N171, uninfected_in_vitro, control_group
|Bronchoalveolar Lavage (BAL) fluid
|tissue: Bronchoalveolar Lavage (BAL) fluid
subject id: patient N171
molecule: Cytoplasmic RNA
|Frozen stocks of virulent Mtb strain H37Rv (#NR-123, BEI resources, Manassas VA) were thawed, cleared of bacterial clumps, and suspended in infecting medium. BAL cells were cultured with H37Rv (3:1 MOI) or medium alone and incubated at 37degC for twenty-four hours.
|Bronchoscopy with BAL was performed by instillation and recovery of up to eight 30 mL aliquots of saline. Following centrifugation, cell pellets were combined, counted and aliquoted.
|Cell pellets were flash-frozen and stored at -80 for eventual RNA extraction.
|Illumina HiSeq 3000
|Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4.b
Gene counts quantitated with Subread:featureCount 1.45 with CPM transformation added with custom Rscripting.
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts-per-million in tab-delimitted text format
|Jan 29, 2023
|Last update date
|Dec 01, 2023
|Case Western Reserve University and the Louis Stokes Cleveland VA Medical Center
|Division of Pulmonary, Critical Care and Sleep Medicine
|10900 Euclid Ave
|Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination