Indexed sequencing libraries were generated from RNA, isolated using TRIzol and without DNAse treatment, as per methods and reagents provided with the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero ribosomal RNA reduction chemistry (Illumina, San Diego, CA). PCR for library generation employed ten cycles. Electrophoresis of the libraries on Bioanalyzer 2100 instrument (Agilent, Santa Clara, CA) showed highest peaks at 220–240 bp. Paired-end multiplexed sequencing of libraries (three per flow cell lane) to generate reads of 101 b was performed on HiSeq 2000 instrument with TruSeq SBS and PE Cluster v3 Kits (Illumina). CASAVA 1.8.2 software (Illumina) was used for base-calling and de-multiplexing, to obtain the raw RNA sequencing reads for further analyses. RNA sequencing of all six samples of this study was performed in one batch.
Ribo zero ribosomal rna reduction chemistry
Manufactured by Illumina
Ribo-Zero ribosomal RNA reduction chemistry is a laboratory technique that selectively removes ribosomal RNA (rRNA) from total RNA samples. This process enriches the sample for non-ribosomal RNA species, such as messenger RNA (mRNA), enabling more sensitive detection and analysis of these target molecules.
Automatically generated - may contain errors
Lab products found in correlation
Truseq stranded total rna library prep kit, by Illumina (2 mentions)
Rs 122 2201, by Illumina (2 mentions)
Casava 1, by Illumina (1 mentions)
Truseq sbs and pe cluster v3 kits, by Illumina (1 mentions)
Truseq stranded total rna sample prep kit, by Illumina (1 mentions)
2100 bioanalyzer, by Agilent Technologies (1 mentions)
Hiseq 2000, by Illumina (1 mentions)
3 protocols using ribo zero ribosomal rna reduction chemistry
1
Stranded RNA Sequencing Library Prep
2
Transcriptomic Profiling of Aged Drosophila
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We collected replicate RNA samples for aged individuals of all five karyotypes of interest; replicate RNA data for young flies are from ref. 22 (link). Additionally, we collected 3 replicate samples for aged male Canton-S, aged XXY females, and aged XYY males, and 4 replicate samples for aged female Canton-S and aged X0 males. After flash-freezing in liquid nitrogen, we dissected and pooled 5 heads from each sample, extracted RNA, and prepared stranded total RNA-seq libraries using Illumina’s TruSeq Stranded Total RNA Library Prep kit with Ribo-Zero ribosomal RNA reduction chemistry, which depletes the highly abundant ribosomal RNA transcripts (Illumina RS-122–2201). We performed single-read sequencing for all total RNA libraries at the Vincent J. Coates Genomic Sequencing Laboratory at UC Berkeley.
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Transcriptomic Profiling of Aged Drosophila
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