Ribosome Fractionation and RNA-seq Analysis
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Corresponding Organization :
Other organizations : Science for Life Laboratory, Karolinska Institutet, Stockholm University, Danish Cancer Society, Karolinska University Hospital, Aarhus University Hospital, Copenhagen University Hospital
Variable analysis
- RNA isolation method (phenol/chloroform extraction and purification with Agencourt AMPure RNAClean XP beads)
- RNA-seq data
- Differential expression (DE) analysis
- Differential translation efficiency (deltaTE) analysis
- RNA source (80S monosomes and polysomes (>3 ribosomes) fractions)
- RNA input amount (100 ng)
- CDNA synthesis (SuperScript IV Reverse Transcriptase)
- DNA purification (Agencourt AMPure XP beads)
- Library preparation (TruSeq Stranded Total RNA library preparation kit and TruSeq RNA Single Indexes)
- Sequencing platform (Illumina NextSeq500)
- Sequencing run (NextSeq 500/550 High Output Kit v2.5 (150 cycles))
- RNA-seq data processing (nf-core/rnaseq pipeline using GRCh37 genome build)
- DE analysis (DESeq2 v1.24.0)
- DeltaTE analysis (deltaTE)
- Positive control: Not specified
- Negative control: Not specified
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