Integrated sRNA-seq and mRNA-seq Library Prep

RNA for sRNA-seq and mRNA-seq was isolated from the same cell-pellet using miRVana total RNA isolation (ThermoFisher, #AM1560). Small RNA-seq libraries were randomly prepared from 400 ng of RNA using the NEXTFLEX Small RNA-Seq Kit v3 (PerkinElmer, #NOVA-5132-05) using 16 PCR cycles. 10 synthetic calibrator RNAs^{44 (link)} were mixed with the input RNA during the first ligation step. mRNA-seq libraries were randomly prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina # RS-122-2101) with 400 ng input RNA. The sequencing libraries were sequenced on the NextSeq 500 System from Illumina.

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Aass K.R., Nedal T.M., Tryggestad S.S., Haukås E., Slørdahl T.S., Waage A., Standal T, & Mjelle R. (2022). Paired miRNA- and messenger RNA-sequencing identifies novel miRNA-mRNA interactions in multiple myeloma. Scientific Reports, 12, 12147.

Publication 2022

miRVana total RNA isolation NEXTFLEX Small RNA-Seq Kit v3 TruSeq Stranded mRNA Library Prep Kit NextSeq 500 System

Cell Isolation Library Ligation Mrna Rna seq

Corresponding Organization :

Other organizations : Norwegian University of Science and Technology, Stavanger University Hospital

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Variable analysis

independent variables

RNA isolation method (miRVana total RNA isolation)
Small RNA-seq library preparation method (NEXTFLEX Small RNA-Seq Kit v3)
MRNA-seq library preparation method (TruSeq Stranded mRNA Library Prep Kit)
Number of PCR cycles (16) for small RNA-seq library preparation

dependent variables

Small RNA-seq data
MRNA-seq data

control variables

Input RNA amount (400 ng) for both small RNA-seq and mRNA-seq library preparation
Synthetic calibrator RNAs (10) added during the first ligation step of small RNA-seq library preparation

controls

Positive control: 10 synthetic calibrator RNAs added during small RNA-seq library preparation
Negative control: Not explicitly mentioned

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