A total of 20 tumour samples with formalin-fixed paraffin-embedded (FFPE) slides were retrieved. RNA was extracted using Trizol (Thermo Fisher Scientific) and isolated using the AllPrep FFPE tissue kit (Qiagen, Germany), following the manufacturer’s instructions. The quality of FFPE-derived RNA was measured by the proportion of fragments >200 b (DV200). FFPE-derived RNA from all 20 samples was processed on FFPE-compatible RNAseq library preparation using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen, USA). RNA sequencing was performed using the QuantSeq 3′ mRNA-sequencing kit (Lexogen, Vienna, Austria) to obtain the gene expression profiles of samples from the IL-6-high and IL-6-low groups.
Allprep ffpe tissue kit
Manufactured by Qiagen
Sourced in Germany
The AllPrep FFPE tissue kit is a laboratory equipment product designed for the extraction and purification of DNA and RNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. The kit provides a standardized workflow for the isolation of high-quality nucleic acids from these challenging sample types.
Automatically generated - may contain errors
2 protocols using allprep ffpe tissue kit
1
Transcriptomic Profiling of FFPE Tumor Samples
2
RNA-seq analysis of FFPE samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
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In the first part of the Cohort Multi and the Cohort Mono, DNA/ RNA was extracted as we previously published using the ALLPrep FFPE tissue kit (Qiagen; ref. 6 ). In the second part of the Cohort Multi, total RNA was extracted from FFPE samples using RNeasy FFPE kit (Qiagen). A total of 150 ng of RNA was used as the starting material for QuantSeq 3 0 mRNA-Seq Library Prep Kit FWD (Lexogen), according to the manufacturer's instructions. RNA-seq reads were mapped using STAR (15) with the proposed ENCODE parameters on the human hg38 genomes and transcript annotation (Ensembl 75). Gene expression profiles were obtained using FeatureCount (16) . The counts per gene were normalized to CPM (counts per million). The CPMnormalized data were then transformed with log 2 using an offset of 1.
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