Protocol detail

RNA-Seq Analysis of Fibroblast Transcriptomes

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Total RNA from Patient, Control, and Unrelated Control fibroblasts (at passage 7) was isolated and quantified as described [35 (link)]. RNA-seq studies were conducted on total RNA (3 to 7 μg) at DNA Link USA, Inc. (San Diego, CA) using poly-A RNA enrichment and library preparation. RNA libraries were sequenced as 75 bp paired-end runs with at least 100 million reads per sample on an Illumina NextSeq 500 platform (Additional File 1: Table S1). The raw RNA-seq data (fastq) was stored and transferred using the BaseSpace Sequence Hub (Illumina, San Diego, CA).

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Widyastuti H.P., Norden-Krichmar T.M., Grosberg A, & Zaragoza M.V. (2020). Gene expression profiling of fibroblasts in a family with LMNA-related cardiomyopathy reveals molecular pathways implicated in disease pathogenesis. BMC Medical Genetics, 21, 152.

Publication 2020

NextSeq 500 BaseSpace Sequence Hub

Fibroblasts Library Patient Poly a rna Rna seq

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Variable analysis

independent variables

Fibroblast cell type (Patient, Control, Unrelated Control)

dependent variables

Total RNA expression profile (as measured by RNA-seq)

control variables

Fibroblast passage number (passage 7)

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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