RNA was extracted from organoids in culture or from OCT embedded frozen hepatoblastoma tumor and adjacent normal liver tissue samples using the miRNeasy Mini Kit (Qiagen, Germantown, MD, USA). Organoids were mechanically disrupted and incubated in organoid harvesting solution (Trevigen, Gaithersburg, MD, USA) at 4 °C for 1 hour prior to extracting RNA. RNA sequencing libraries were generated using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero ribosomal RNA depletion (Illumina, San Diego, CA, USA). Libraries were sequenced with 2 × 150 bp paired-end reads on an Illumina NextSeq system.
Ribo zero ribosomal rna depletion
Manufactured by Illumina
Sourced in United States
Ribo-Zero ribosomal RNA depletion is a laboratory technique used to remove ribosomal RNA (rRNA) from RNA samples. Ribosomal RNA typically accounts for a large portion of the total RNA content in a sample, and its removal can enhance the detection and analysis of other RNA species, such as messenger RNA (mRNA) and non-coding RNA.
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Lab products found in correlation
2 protocols using ribo zero ribosomal rna depletion
1
RNA Extraction and Sequencing from Organoids and Tumor Samples
2
Cardiac Gene Expression Profiling in Kv1.5 Knockout Mice
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We performed RNA-seq on Kv1.5−/− sham mice and Kv1.5−/− mice exhibiting TTS. The differences in expression observed with RNA seq were confirmed by RT-PCR.33 (link) Ribonucleic Acid (RNA) was isolated from the apex and base of heart samples using the miRNeasy Mini Kit (Qiagen, Cat No./ID: 217004) according to the manufacturer’s instruction. RNA quality was measured with Agilent RNA 6000 Nano Kit (5067–1511). Contaminating Deoxyribonucleic Acid (DNA) was degraded by a 15-min incubation with RNase-free DNase.
RNA-seq was performed as described.34 (link) RNA-seq libraries were prepared using TruSeq stranded total RNA sample prep kit with Ribo-Zero ribosomal RNA depletion (Illumina) according to the protocols of the manufacturer. NextSeq 500 high output V2 kit (FC-404-2002) was used for sequencing on the NextSeq 550 sequencing system. RNA-seq data analysis with STAR + cufflink combination and gene set enrichment analysis was performed at Case Western Reserve University Computational Biology Core. Real-time-PCR was performed to confirm significant differences observed in RNA expression based on the sequencing analysis. The supplement contains the details of these procedures and the primer IDs.
RNA-seq was performed as described.34 (link) RNA-seq libraries were prepared using TruSeq stranded total RNA sample prep kit with Ribo-Zero ribosomal RNA depletion (Illumina) according to the protocols of the manufacturer. NextSeq 500 high output V2 kit (FC-404-2002) was used for sequencing on the NextSeq 550 sequencing system. RNA-seq data analysis with STAR + cufflink combination and gene set enrichment analysis was performed at Case Western Reserve University Computational Biology Core. Real-time-PCR was performed to confirm significant differences observed in RNA expression based on the sequencing analysis. The supplement contains the details of these procedures and the primer IDs.
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