Rrna Depletion
Rrna Depletion - Related Videos
06:21
Depletion of Ribosomal RNA for Mosquito Gut Metagenomic RNA-seq
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Cited by 20 •
2013
A ribosomal RNA (rRNA) depletion protocol was developed to enrich messenger RNA (mRNA) for RNA-seq of the mosquito gut metatranscriptome. Sample specific rRNA probes, which were used to remove rRNA via subtraction, were created from the mosquito and its gut microbes. Performance of the protocol can result in the removal of approximately 90-99% of rRNA.
06:17
Depletion of Specific Cell Populations by Complement Depletion
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Cited by 15 •
2010
To effectively study the function of immune cell populations their purification is often required. Complement depletion is a fast and inexpensive technique for the isolation of immune cell populations with high purity.
10:57
16S rRNA Sequencing: A PCR-based Technique to Identify Bacterial Species
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2023
Source: Ewa Bukowska-Faniband1, Tilde Andersson1, Rolf Lood1 1 Department of Clinical Sciences Lund, Division of Infection Medicine, Biomedical Center, Lund University, 221 00 Lund, Sweden Planet Earth is a habitat for millions of bacterial species, each of which has specific characteristics. Identification of bacterial species is widely used in microbial ecology to determine biodiversity of environmental samples and medical microbiology to diagnose infected patients. Bacteria can be classified...
08:50
Depletion and Reconstitution of Macrophages in Mice
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Cited by 118 •
2012
Macrophages play a central role in homeostasis and pathology in many tissues. The protocol presented here describes methods for depleting macrophages in vivo, deriving polarized macrophages from bone marrow aspirates, and adoptively transferring macrophages into mice. These techniques allow determination of the role that polarized macrophages play in health and disease.
11:07
Macrophage Cholesterol Depletion and Its Effect on the Phagocytosis of Cryptococcus neoformans
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Cited by 22 •
2014
In this article, a protocol for infection of macrophages with Cryptococcus neoformans is described. Also, a method for sterol depletion from the macrophages is explained. These protocols provide a guide to study fungal infections in vitro and examine the role of sterols in such infections.
FAQs
Probe sequences are designed to match ribosomal RNA, so they hybridize preferentially with those molecules in the total RNA sample. This creates RNA-DNA or RNA-RNA hybrids that can be targeted for removal, while transcripts lacking the matching rRNA sequences remain available. Probe complementarity therefore determines which RNA population is depleted and how broadly other transcripts are retained.
Poly(A)-based approaches favor transcripts carrying polyadenylated tails, whereas rRNA depletion does not depend exclusively on that feature. It can therefore preserve messenger RNA and noncoding RNA populations that may be missed when selection is limited to polyadenylated molecules. This distinction is important when the goal is broader transcriptome representation rather than preferential analysis of one RNA class.
Both strategies remove rRNA after probe hybridization, but they use different mechanisms. RNase H digestion targets the RNA within RNA-DNA hybrids, whereas affinity-based capture removes the hybrids through a binding step. In either case, the key outcome is depletion of probe-bound ribosomal sequences before the remaining RNA enters sequencing library preparation.
The workflow begins with a total RNA sample and complementary oligonucleotide probes directed against rRNA sequences. After hybridization, the resulting RNA-DNA or RNA-RNA hybrids are removed either by RNase H digestion or affinity-based capture. The RNA that remains is then available for library preparation and sequencing, allowing analysis beyond the dominant ribosomal fraction.
This approach is particularly useful for degraded RNA samples and for RNA populations that lack polyadenylation. Because it does not rely exclusively on poly(A) tails, it can retain a wider range of transcripts under those conditions. Researchers can consequently examine gene expression and regulatory RNA in samples where poly(A)-dependent enrichment would provide less complete representation.
In genetics, rRNA-depleted libraries support transcriptome profiling by improving access to messenger RNA and noncoding RNA after abundant rRNA has been reduced. The resulting data can be used to study gene expression patterns and regulatory transcripts while representing more diverse RNA populations. This broader coverage is valuable when transcript regulation extends beyond conventional protein-coding messages.