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Sample GSM7009640 Query DataSets for GSM7009640
Status Public on Dec 01, 2023
Title patient N162, uninfected_in_vitro, control_group
Sample type SRA
 
Source name Bronchoalveolar Lavage (BAL) fluid
Organism Homo sapiens
Characteristics tissue: Bronchoalveolar Lavage (BAL) fluid
subject id: patient N162
treatment: uninfected_in_vitro
group: control_group
molecule: Cytoplasmic RNA
Treatment protocol 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.
Growth protocol 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.
Extracted molecule total RNA
Extraction protocol Cell pellets were flash-frozen and stored at -80 for eventual RNA extraction.
RiboZero v1
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description N162_mediarested_control
TAAGTGC-CAGCCCA_N162_mediarested_control
Data processing 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
 
Submission date Jan 29, 2023
Last update date Dec 01, 2023
Contact name Richard Silver
E-mail(s) rfs4@case.edu
Organization name Case Western Reserve University and the Louis Stokes Cleveland VA Medical Center
Department Division of Pulmonary, Critical Care and Sleep Medicine
Street address 10900 Euclid Ave
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
 
Platform ID GPL21290
Series (1)
GSE223999 Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination
Relations
BioSample SAMN32955021
SRA SRX19212351

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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