Hepatic transcriptome analysis was performed by RNA sequencing on RNA extracts from terminal liver samples (15 mg fresh tissue), as described in detail previously[19 (link)]. The RNA quantity was measured using Qubit® (Thermo Scientific, Eugene, OR, United States). The RNA quality was determined using a bioanalyzer with RNA 6000 Nano kit (Agilent, Waldbronn, Germany). RNA sequence libraries were prepared with NeoPrep (Illumina, San Diego, CA, United States) using Illumina TruSeq stranded mRNA Library kit for NeoPrep (Illumina, San Diego, CA, United States) and sequenced on the NextSeq 500 (Illumina, San Diego, CA, United States) with NSQ 500 hi-Output KT v2 (75 CYS, Illumina, San Diego, CA, United States). Reads were aligned to the GRCm38 v84 Ensembl Mus musculus genome using STAR v.2.5.2a with default parameters[36 (link)]. Differential gene expression analysis was performed with DEseq2[37 (link)]. Genes with a Benjamini and Hochberg adjusted P ≤ 0.05 (5% False Discovery Rate) were regarded as statistically significantly regulated. Enrichment analysis of KEGG pathways were performed using the clusterProfiler package for R[38 (link)].
Protocol detail
Hepatic Transcriptome Profiling by RNA-Seq
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization :
Other organizations : Gubra (Denmark), Novo Nordisk Foundation, University of Copenhagen
Top 5 similar protocols
Protocol cited in 1 other protocol
Variable analysis
independent variables
- None explicitly mentioned
- Hepatic transcriptome (gene expression)
- RNA quantity measured using Qubit
- RNA quality determined using bioanalyzer with RNA 6000 Nano kit
- RNA sequence libraries prepared with NeoPrep using Illumina TruSeq stranded mRNA Library kit
- Sequencing performed on the NextSeq 500 with NSQ 500 hi-Output KT v2 (75 CYS)
- Reads aligned to the GRCm38 v84 Ensembl Mus musculus genome using STAR v.2.5.2a with default parameters
- Differential gene expression analysis performed with DEseq2
- Genes with a Benjamini and Hochberg adjusted P ≤ 0.05 (5% False Discovery Rate) regarded as statistically significantly regulated
- Enrichment analysis of KEGG pathways performed using the clusterProfiler package for R
- No positive or negative controls were explicitly mentioned in the provided information.
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!