Computational protocol: Single-cell differences in matrix gene expression do not predict matrix deposition

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Protocol publication

[…] Poly-adenylated RNA from passage 1 clonal MSCs populations were isolated from monolayer culture in basal media. The Qiagen miRNeasy kit was used for RNA isolation, the NEB Next Poly(A) mRNA Magnetic Isolation Module was used for selection of poly-adenylated transcripts and NEB Next Ultra Library Preparation Kit for Illumina was used for library preparation. Each sample was sequenced with 50-bp single-end reads on an Illumina HiSeq and to a depth of 15–25 M reads. Reads were aligned to bosTau7 using STAR. Reads per gene were quantified using HTSeq and a RefSeq bosTau7 from annotation release 103 (ref. ). FPKM (fragments per kilobase of transcript per million mapped reads) for each gene was calculated using R. […]

Pipeline specifications

Software tools STAR, HTSeq
Application RNA-seq analysis