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Series GSE114371 Query DataSets for GSE114371
Status Public on Jun 06, 2018
Title AmpliSeq Transcriptome Analysis of Human Alveolar and Monocyte-Derived Macrophages Over Time in Response to Mycobacterium tuberculosis infection
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Mycobacterium tuberculosis (M.tb) infection, and human blood monocyte-derived macrophages (MDM) are a model for investigating M.tb-macrophage interactions. Here, we use a targeted RNA-Seq method to measure transcriptome-wide changes in RNA expression patterns of freshly obtained HAM (used within 6 h) and 6 day cultured MDM upon M.tb infection over time (2, 24 and 72 h), in both uninfected and infected cells from three donors each. The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) uses primers targeting 18,574 mRNAs and 2,228 non-coding RNAs (ncRNAs) for a total of 20,802 transcripts. AmpliSeqTM yields highly precise and reproducible gene expression profiles (R2 >0.99). Taking advantage of AmpliSeq’s reproducibility, we establish well-defined quantitative RNA expression patterns of HAM versus MDM, including significant M.tb-inducible genes, in networks and pathways that differ in part between MDM and HAM. A similar number of expressed genes are detected at all time-points between uninfected MDM and HAM, in common pathways including inflammatory and immune functions, but canonical pathway differences also exist. In particular, at 2 h, multiple genes relevant to the immune response are preferentially expressed in either uninfected HAM or MDM, while the HAM RNA profiles approximate MDM profiles over time in culture, highlighting the unique RNA expression profile of freshly obtained HAM. MDM demonstrate a greater transcriptional response than HAM upon M.tb infection, with 2 to >10 times more genes up- or down-regulated. The results identify key genes involved in cellular responses to M.tb in two different human macrophage types. Follow-up bioinformatics analysis indicates that approximately 30% of response genes have expression quantitative trait loci (eQTLs in GTEx), common DNA variants that can influence host gene expression susceptibility or resistance to M.tb, illustrated with the TREM1 gene cluster and IL-10.
Overall design Assessment of transcriptome profiles from cells infected with Mycobacterium tuberculosis using AmpliSeq.
Contributor(s) Sadee W, Schlesinger LS, Papp A, Azad A, Pietrzak M
Citation(s) 29847580
Submission date May 11, 2018
Last update date Mar 01, 2019
Contact name Maciej Pietrzak
Phone +1(614) 688 9721
Organization name Ohio State University
Department Department of Biomedical Informatics College of Medicine
Street address 1800 Cannon Drive, 340C Lincoln Tower
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
Platforms (1)
GPL17303 Ion Torrent Proton (Homo sapiens)
Samples (36)
GSM3140512 HAM Donor 7 2h Control
GSM3140513 HAM Donor 7 2h Mtb
GSM3140514 HAM Donor 7 24h Control
BioProject PRJNA471095
SRA SRP145502

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Supplementary file Size Download File type/resource
GSE114371_FeatureCounts.txt.gz 860.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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