Fig. 1
From: TIRE-seq simplifies transcriptomics via integrated RNA capture and library preparation
TIRE-seq outperforms Prime-seq on cell lysates. (a) Overview of the TIRE-seq workflow. Cells are lysed directly in media and transferred to Qiagen TurboCapture plates. mRNA hybridizes to immobilized poly-T oligos, followed by washing and reverse transcription. After well barcoding, samples are pooled, and library preparation occurs on the pooled material. Gene expression is quantified using 5’ tag sequencing. (b) Read mapping statistics for Prime-seq, TIRE-seq, and TruSeq (GSE122633). “Intact cells” refers to FACS-sorted cells. “Lysate” refers to crude homogenized lysates, and “Purified RNA” refers to RNA purified using silica columns. (c) Downsampling analysis of 11 ng Universal Human Reference RNA (UHRR). Janjic = E-MTAB-10139, TruSeq = GSE47774. Top: Median number of genes detected. Bottom: Median number of unique molecules (UMIs) detected. Error bars represent the median absolute deviation of replicates. (d) Performance of TIRE-seq on 10,000 cell equivalents from HEK293T cell lysates. TruSeq = GSE122633. (e) Pearson correlation of logCPM for UHRR replicates across protocols. (g) Binned transcript coverage across protocols. ShortRead = Illumina 70-nt tag sequencing. LongRead = Oxford Nanopore sequencing of full-length Prime-seq cDNA.
