NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE125287 Query DataSets for GSE125287
Status Public on Jun 12, 2019
Title Gene expression analysis of mouse alveolar macrophages infected with Mycobacterium tuberculosis
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The aim of this study was to measure the immune response of alveolar macrophages (AMs) to intracellular Mtb infection in vivo. We characterized the transcriptional profile of murine Mtb-infected AMs after aerosol infection by sorting cells from bronchoalveolar lavage fluid and performing low-input RNA-sequencing. To determine the effect of the transcription factor Nrf2 on this response we also measured the transcriptional profiles of AMs from mice lacking Nrf2.
 
Overall design To characterize the early macrophage transcriptional response to Mtb infection, we infected mice with 2000-4000 CFU of mEmerald-H37Rv, and isolated AMs (CD45+, Zombie Violet-, CD3-/CD19-, Siglec-F+, CD11bmid, and CD64+) from BAL by fluorescence activated cell sorting at various time points over the first 10 days following infection. Three populations were sorted for analysis by RNA-seq: Mtb-infected AMs (mEmerald+), bystander AMs (mEmerald-), and AMs from naïve mice. As a comparison, we repeated the high-dose infections using an mEmerald-expressing strain of Mtb lacking the RD1 virulence locus (deltaRD1-H37Rv) and using fluorescent 1uM carboxylate-coated latex beads.
 
Contributor(s) Rothchild AC, Diercks AH, Aderem A
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jan 17, 2019
Last update date Jun 12, 2019
Contact name Aderem Lab
E-mail(s) alan.diercks@seattlechildrens.org
Organization name Seattle Children's Research Institute
Lab Aderem Lab
Street address 307 Westlake Avenue North, Suite 500
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (54)
GSM3567744 B6.bead.naive.24.AD51617
GSM3567745 B6.H37Rv.naive.24.AD13
GSM3567746 B6.bead.beadPos.24.AD51617
Relations
BioProject PRJNA515746
SRA SRP180017

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE125287_rawCounts.tsv.gz 1.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap