RNA-seq Analysis of HIV Infection

RNA-seq was performed on 5 HIV-seronegative and 10 HIV-infected subjects. Library construction and sequencing were performed by the Genomics and Microarray Core Facility at the University of Colorado Anschutz Medical Campus as previously described (38 (link)). RNA quality and integrity was first assessed using an Agilent TapeStation 2200. The library was constructed using the Illumina TruSeq mRNA library construction kit. Single-end sequencing was performed using an Illumina HiSeq 4000 for 125 cycles. RNA-seq data have been deposited in the Sequence Read Archive database (http://www.ncbi.nlm.nih.gov/bioproject/496501). Sequencing data were processed using the Illumina BaseSpace online platform and assessed using FASTQC. The FASTQ Toolkit tool was used to filter, adaptor trim, and quality trim reads. Alignment to the hg19 reference genome was performed using the TopHat Alignment tool, with assembly and differential expression analysis performed using the Cufflinks Assembly & Differential Expression tool.

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.

Neff C.P., Atif S.M., Logue E.C., Siebert J., Görg C., Lavelle J., Fiorillo S., Twigg H., Campbell T.B., Fontenot A.P, & Palmer B.E. (2020). HIV infection is associated with loss of anti-inflammatory alveolar macrophages. Journal of immunology (Baltimore, Md. : 1950), 205(9), 2447-2455.

Publication 2020

TapeStation 2200 TruSeq mRNA library construction kit HiSeq 4000 BaseSpace online platform

Genome Library Microarray Mrna Rna seq

Corresponding Organization :

Other organizations : University of Colorado Anschutz Medical Campus, University Hospital and Clinics, Indiana University – Purdue University Indianapolis

Top 5 similar protocols

Variable analysis

independent variables

HIV serostatus (HIV-seronegative vs. HIV-infected)

dependent variables

Gene expression levels

control variables

RNA quality and integrity assessed using Agilent TapeStation 2200
Library construction using Illumina TruSeq mRNA library construction kit
Single-end sequencing using Illumina HiSeq 4000 for 125 cycles
Data processing using Illumina BaseSpace online platform, FASTQC, FASTQ Toolkit, TopHat Alignment, and Cufflinks Assembly & Differential Expression

controls

The study included 5 HIV-seronegative subjects as a negative control group

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.

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?

Revolutionizing how scientists
search and build protocols!