The isolation and sequencing analysis of AIS clot RNA is described in detail in a previous paper.10 (link) In brief, clot RNA was isolated via a modified magnetic bead capture protocol for the PerkinElmer Chemagic 360, and eluted into a final volume of 140 uL. Before library preparation, RNA concentration was remeasured via Qbit Assay (Invitrogen, Carlsbad, CA) with a TBS-380 Fluorometer (Promega, Madison, WI) and the quality of the RNA was measured on an Agilent 2400 Tape Station (Agilent, Las Vegas, NV). RNA samples that were not completely degraded on inspection of the electrophoresis gel, we subjected to library preparation via the Illumina TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA). RNA libraries were subjected to 100-cycle, paired-end sequencing on the NovaSeq6000 system (Illumina, San Diego, CA, USA) and analyzed as previously described. Aggregate quality control data (i.e. alignment statistics and feature assignment statistics) were summarized in MultiQC.
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Isolation and Sequencing of AIS Clot RNA
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Corresponding Organization : University at Buffalo, State University of New York
Other organizations : Jacobs (United States), University of California, Los Angeles, Massachusetts General Hospital, Brigham and Women's Hospital
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Variable analysis
independent variables
- Modified magnetic bead capture protocol for the PerkinElmer Chemagic 360 used to isolate clot RNA
- RNA concentration measured via Qbit Assay
- RNA quality measured on an Agilent 2400 Tape Station
- Sequencing of RNA libraries using 100-cycle, paired-end sequencing on the NovaSeq6000 system
- Aggregate quality control data (i.e., alignment statistics and feature assignment statistics) summarized in MultiQC
- Elution of clot RNA into a final volume of 140 uL
- Positive control: RNA samples that were not completely degraded on inspection of the electrophoresis gel were subjected to library preparation
- Negative control: Not explicitly mentioned
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