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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 06, 2019 |
| Title |
Whole lung transcriptomics of a house dust mite model of mild/moderate asthma |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Purpose: Identify whole lung gene expression patterns in a house dust mite model of mild/moderate asthma
Methods: Lung gene expression profiles of 10 week old BALB/c female mice were generated by ribosome-depleted, 150 nt, paired-end, stranded RNA-seq with Illumina HiSeq v4. Sequence reads that passed quality filters after trimming were analyzed with Sailfish-cir to identify linear RNAs and circular RNAs. Differential expression of linear RNAs was assessed with Deseq2 . QRT–PCR validation was performed using TaqMan and SYBR Green methods.
Results: 100 million sequence reads per sample were mapped to the mouse genome (build mm10) using Sailfish-cir to identify linear and circular RNA transcripts. Pathway analysis of differentially expressed genes identified upregulation of gene sets for human asthma, mouse lung allergic inflammation, Muc5ac regulated genes and smooth muscle genes after allergic sensitization. Gene level exppression in each asthma-related pathway was reduced by the miR-145 antagonist. The miR-145 antagonist and several nontargeting oligos also upregulated interferon signaling pathways suggesting a general antiinflammatory effect of LNA/DNA oligos in the lung.
Conclusions: Lung-directed delivery of LNA/DNA oligonucleotides with cationic lipid nanoparticles is an efffective means to prevent inflammatory gene expression in a house dust mite model of mild/moderate asthma.
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| Overall design |
Linear and circular RNA transcript expression was compared in whole lung tissue from unsensitized, house dust mite sensitzed, antimiR-145 treated treated mice
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| Contributor(s) |
Ramelli SC, Zhou T, Gerthoffer WT |
| Citation(s) |
32044723 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 HL077726 |
Small heat shock proteins in smooth muscle plasticity |
UNIVERSITY OF SOUTH ALABAMA |
William T Gerthoffer |
| R21 AI116985 |
MICRORNA REGULATION OF AIRWAY REMODELING AND REPAIR IN ASTHMA |
UNIVERSITY OF SOUTH ALABAMA |
William T Gerthoffer |
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| Submission date |
Jun 05, 2019 |
| Last update date |
Feb 15, 2020 |
| Contact name |
William T Gerthoffer |
| E-mail(s) |
wgerthoffer@med.unr.edu
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| Phone |
7752293028
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| Organization name |
University of Nevada, Reno
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| Department |
Pharmacology
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| Lab |
Gerthoffer
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| Street address |
1440 N Virginia St
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| City |
Reno |
| State/province |
Nevada |
| ZIP/Postal code |
89509 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (31)
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| GSM3855105 |
Lung, Saline 10 |
| GSM3855106 |
Lung, Saline 11 |
| GSM3855107 |
Lung, HDM 1 |
| GSM3855108 |
Lung, HDM 2 |
| GSM3855109 |
Lung, HDM 3 |
| GSM3855110 |
Lung, HDM 4 |
| GSM3855111 |
Lung, HDM 5 |
| GSM3855112 |
Lung, HDM 7 |
| GSM3855113 |
Lung, HDM 8 |
| GSM3855114 |
Lung, HDM 9 |
| GSM3855115 |
Lung, HDM 17 |
| GSM3855116 |
Lung, HDM 18 |
| GSM3855117 |
Lung, AM 1 |
| GSM3855118 |
Lung, AM 2 |
| GSM3855119 |
Lung, AM 3 |
| GSM3855120 |
Lung, AM 4 |
| GSM3855121 |
Lung, AM 5 |
| GSM3855122 |
Lung, AM 6 |
| GSM3855123 |
Lung, AM 7 |
| GSM3855124 |
Lung, AM 8 |
| GSM3855125 |
Lung, AM 9 |
| GSM3855126 |
Lung, AM 10 |
| GSM3855127 |
Lung, Dex_HDM 1 |
| GSM3855128 |
Lung, Dex_HDM 2 |
| GSM3855129 |
Lung, Dex_HDM 3 |
| GSM3855130 |
Lung, Dex_HDM 4 |
| GSM3855131 |
Lung, Dex_HDM 5 |
| GSM3855132 |
Lung, Dex_HDM 6 |
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| Relations |
| BioProject |
PRJNA547063 |
| SRA |
SRP200563 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE132263_HDM_circularRNA_tpm.txt.gz |
231.6 Kb |
(ftp)(http) |
TXT |
| GSE132263_HDM_linearRNA_tpm.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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