Comprehensive RNA Sequencing of Primate Samples

RNA for 499 samples was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kits (Thermo Fisher), and RNA from 48 samples was extracted using the PAXgene Blood RNA Kit IVD (Qiagen) following the standard protocols for each procedure. RQN was quantified using AATI Fragment Analyzer. RNA sequencing libraries were prepared using 50 ng of total RNA and following a recently developed 3′-biased protocol, TM3′SEq. (74 (link)). Libraries were amplified with 16 PCR cycles. All other procedures followed the published protocol or manufacturer recommendations. Libraries were combined in equimolar quantities and sequenced on an Illumina NovaSeq S2 flowcell (R1 was 25 bp and R2 was 80 bp to capture the complementary DNA [cDNA] transcript) to an average read depth of 3.5 million reads per sample. We mapped cDNA reads to the M. mulatta reference assembly Mmul_10 using kallisto (75 (link)) (average mapping rate = 71.1%).

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.

Watowich M.M., Chiou K.L., Montague M.J., Simons N.D., Horvath J.E., Ruiz-Lambides A.V., Martínez M.I., Higham J.P., Brent L.J., Platt M.L, & Snyder-Mackler N. (2022). Natural disaster and immunological aging in a nonhuman primate. Proceedings of the National Academy of Sciences of the United States of America, 119(8), e2121663119.

Publication 2022

PAXgene Blood RNA Kit IVD NovaSeq S2 flowcell

Blood Cdna Isolation

Corresponding Organization : University of Washington

Other organizations : University of Pennsylvania, Duke University, North Carolina Central University, North Carolina Museum of Natural Sciences, North Carolina State University, University of Puerto Rico System, New York University, New York Consortium in Evolutionary Primatology, University of Exeter

Top 5 similar protocols

Variable analysis

independent variables

RNA extraction method (MagMAX for Stabilized Blood Tubes RNA Isolation Kits or PAXgene Blood RNA Kit IVD)

dependent variables

RQN (RNA Quality Number) quantified using AATI Fragment Analyzer
Read depth (average 3.5 million reads per sample)
Mapping rate (average 71.1%)

control variables

Amount of total RNA used for library preparation (50 ng)
Library preparation protocol (3'-biased TM3'SEq protocol)
Number of PCR cycles for library amplification (16 cycles)
Sequencing platform (Illumina NovaSeq S2 flowcell)
Read length (R1 = 25 bp, R2 = 80 bp)
Reference genome assembly (M. mulatta Mmul_10)

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!