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

PROVIDER: PRJNA342099 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4188530_1.fastq.gz	Fastqsanger.gz
	SRR4188530_2.fastq.gz	Fastqsanger.gz
	SRR4188540_1.fastq.gz	Fastqsanger.gz
	SRR4188540_2.fastq.gz	Fastqsanger.gz
	SRR4188550_1.fastq.gz	Fastqsanger.gz

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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 either Pkd1f/f, Pkd1f/f:HoxB7-Cre mice or Pkd2f/f, Pkd2f/f:HoxB7-Cre mice

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-01-26 | GSE86509 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of pancreatic tissue transcriptomes from KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice treated with caerulein

Project description:Purpose: we used next generation sequencing to analyze gene expression profiles of pancreatic tissues from KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice treated with caerulein. The goals of this study are to compare the different gene expression profiles of pancreatic tissue between KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice treated with caerulein.

2021-06-11 | GSE176571 | GEO

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Project description:Conclusion: Elf4fl/fl-Villin-Cre mice are more sensitive to alcohol induced liver steatosis

2022-05-18 | GSE192923 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Il17ra villin cre -/+ colon transcriptomes at day 10 post C. rodentium infection

Project description:We report analysis of colonic transcriptome in gut epithelial cells specific deficient mouse (Il17ra villin cre +) and littermate control mouse (Il17ra villin cre -) infected with Citrobater rodentium (C. rodentium) for 10 days. We found RNA-seq data show Nox family genes and defensin genes are downregulated in Il17ra villin cre + mice. It is interestingly Tnfsf13 was also downregulated in Il17ra villin cre + mice. These genes expressions were confirmed by qRT–PCR validation was performed using TaqMan assays. Finally, this study provides first detailed analysis of C. rodentium infected colonic transctiptome in Il17ra villin cre + mice, with biologic replicates, generated by RNA-seq technology.

2020-12-08 | GSE160157 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of pancreatic tissue transcriptomes from KrasG12D Pdx1-Cre and miR-301a-/- KrasG12D Pdx1-Cre mice treated with caerulein

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Elf4fl/fl-Villin-Cre distal colon Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Brown adipocytes transcriptomes from Control (LrpprcFF) and LrpprcBKO (LrpprcFF, Ucp1-CRE) mice

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Identification of mRNAs modulated by the HOXB7-MEK signaling cascade

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