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Next Generation Sequencing Facilitates Quantitative Analysis of either Pkd1f/f, Pkd1f/f:HoxB7-Cre mice or Pkd2f/f, Pkd2f/f:HoxB7-Cre mice

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE86509 | GEO | 2018/01/26

REPOSITORIES: GEO

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Next Generation Sequencing Facilitates Quantitative Analysis of either Pkd1f/f, Pkd1f/f:HoxB7-Cre mice or Pkd2f/f, Pkd2f/f:HoxB7-Cre mice smallRNA [miRNA-seq]

Project description:Purpose: To reveal the cystogenesis regulatory mechanism by miRNA and miRNA targeted genes in ADPKD mouse models. Method(miRNA-seq): Small RNA sample preparation was done according to Illumina’s protocol. In brief, 5’ and 3’ adapters were sequentially ligated to small RNA of 18–30 bases gel purified from 5–10 µ total RNA. Adapter-ligated small RNA was reverse transcribed, amplified and sequenced on a HiSeq2000 (Illumina) following manufacturer's instructions. Raw data (the reads for each miRNA) were normalized to the total reads of each individual sample as the standardized to reads per (RPM; miRNA counts / total count of each sample x 1 million). Method(common): Both miRNA-seq and RNA-seq were carried out using the kidney tissues from two mouse models at postnatal day 1, 3 and 7 in triplicate samples. Total RNA was isolated using TRIzol method according to manufacturer’s protocol (Invitrogen Life Technologies). Result: UIn RNA-seq analysis, total 3,040 transcripts in Pkd1f/f:HoxB7-cre mice and 2,470 transcripts in Pkd2f/f:HoxB7-cre mice were differentially expressed at indicated time points (FDR<0.05). In addition, we also identified 1,297 common transcripts in both mouse models. In miRNA analysis, total 243 of miRNAs were identified as differentially expressed genes while 130 miRNAs were common in both mouse models. Among common miRNAs, total 13 miRNAs including 11 upregulated and 2 downregulated miRNAs were selected based on comparison of expression patterns at each time point. Conclusion: Our study described the parallel integrated analysis of miRNA-seq and RNA-seq data and validated the expression, direct interaction and cystogenesis-related functions of key miRNAs and mRNA targets.

2018-01-26 | GSE86508 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of either Pkd1f/f, Pkd1f/f:HoxB7-Cre mice or Pkd2f/f, Pkd2f/f:HoxB7-Cre mice transcriptome [RNA-seq]

Project description:Purpose: To reveal the cystogenesis regulatory mechanism by miRNA and miRNA targeted genes in ADPKD mouse models. Method (mRNA-seq): In order to construct cDNA libraries with the TruSeq RNA library kit, 1ug of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq2000. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using an Agilent Technologies 2100 Bioanalyzer. The transcript counts in isoform level and gene level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks. Method (common): Both miRNA-seq and RNA-seq were carried out using the kidney tissues from two mouse models at postnatal day 1, 3 and 7 in triplicate samples. Total RNA was isolated using TRIzol method according to manufacturer’s protocol (Invitrogen Life Technologies). Result: UIn RNA-seq analysis, total 3,040 transcripts in Pkd1f/f:HoxB7-cre mice and 2,470 transcripts in Pkd2f/f:HoxB7-cre mice were differentially expressed at indicated time points (FDR<0.05). In addition, we also identified 1,297 common transcripts in both mouse models. In miRNA analysis, total 243 of miRNAs were identified as differentially expressed genes while 130 miRNAs were common in both mouse models. Among common miRNAs, total 13 miRNAs including 11 upregulated and 2 downregulated miRNAs were selected based on comparison of expression patterns at each time point. Conclusion: Our study described the parallel integrated analysis of miRNA-seq and RNA-seq data and validated the expression, direct interaction and cystogenesis-related functions of key miRNAs and mRNA targets.

2018-01-26 | GSE86507 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cardiac-specific Bmi1 deletion

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-01-30 | E-GEOD-65447 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of ApoE-/-/SAHHWT, ApoE-/-/SAHH+/- mice and ApoE-/-/SAHH+/- +Betaine mice