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Series GSE69186 Query DataSets for GSE69186
Status Public on Mar 09, 2016
Title Small and large RNA sequencing of mouse livers receiving small hairpin RNAs
Organisms Homo sapiens; Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Adeno-associated viral (AAV) small hairpin (shRNA) expression vectors are a promising therapeutic but can induce severe liver toxicity when delivered at high albeit undefined doses. Using various AAV-shRNA vectors under the high-expressing U6 and low-expressing H1 promoters, we found that dose-limiting toxicity was strongly correlated with an shRNA concentration of >12% of total microRNA levels. Toxicity was associated with a specific reduction in the first synthesized 22nt isoform of miR-122-5p, resulting in the specific de-repression of miR-122 target mRNAs. A causative link between miR-122 reduction and toxicity was established when an AAV-sh-miR-122 vector producing >20% of the total liver miRNAs prevented liver toxicity. Consistent with these results, miR-122 knockout mice, which in part adapt to an absence of miR-122 reduction, also show no toxicity with high dose AAV-shRNA delivery.
Overall design RNA sequencing of 12 liver samples, 2 receiving H1-shRNAs, 7 with U6-shRNAs and 3 controls; small RNA sequencing of 95 samples including 18 with CMV-driven miR-122 expression in HEK293 cells, 13 in miR-122 knockout mice, 9 samples in mice heterozygous for miR-122, 5 samples with Cre-mediate excision of miR-122, 19 samples immunoprecipitated with Ago2 and 31 additional liver samples (3 control, 11 receiving H1-shRNAs and 17 receiving U6-shRNAs). Small RNA libraries were barcoded (first 4 nucleotides) at the 5' end and ligated to linker-1 (5'-CTGTAGGCACCATCAAT) at the 3' end.
Contributor(s) Valdmanis PN, Kay MA
Citation(s) 27064447
Submission date May 22, 2015
Last update date May 15, 2019
Contact name Paul Valdmanis
Phone 206-221-8059
Organization name University of Washington
Department Medicine
Lab Paul Valdmanis
Street address 1705 NE Pacific St, HSB J-309
City Seattle
State/province WA
ZIP/Postal code 98115-7720
Country USA
Platforms (4)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (107)
GSM1694991 liver_control_rep1
GSM1694992 liver_control_rep2
GSM1694993 liver_U6-sh-hAAT_25nt_rep1
BioProject PRJNA284768
SRA SRP058652

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69186_Ago2IP_smallRNA_RPM.txt.gz 12.9 Kb (ftp)(http) TXT
GSE69186_CMV_miR_122_matches.txt.gz 512 b (ftp)(http) TXT
GSE69186_liver_shRNA_FPKM.txt.gz 709.0 Kb (ftp)(http) TXT
GSE69186_total_shRNA_smallRNA_RPM.txt.gz 39.2 Kb (ftp)(http) TXT
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Processed data are available on Series record

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