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$\begingroup$ I want to filter out ribosomal RNA from scRNA-seq data (downloaded from here). Is there a list of known ribosomal RNA? The only solution I found is SortMeRNA, however it works with raw sequencing data afaik, while I already have a matrix with transcript counts for each cell. I searched for a comprehensive list of rRNAs but I didn't find any. terdon 7, 296 2 gold badges 11 silver badges 34 bronze badges asked Jan 2 '18 at 21:49 $\endgroup$ 2 The rRNA genes in that dataset are Rn45s and Rn4. 5s. BTW, you have gene counts, not transcript counts. answered Jan 2 '18 at 22:42 Devon Ryan ♦ Devon Ryan 18. 2k 2 gold badges 21 silver badges 48 bronze badges 5 In the paper mentioned, we used the ScaleData function in Seurat to regress out the number of reads, Rn45s abundance, and percent ribosomal gene transcripts. Ribosomal genes were found with the regular expression ^Rp[sl][[:digit:]]. tiss <- ScaleData(object = tiss, = c("nReads", "", "Rn45s")) Here's a fuller notebook, and we'll have a better organized repository soon.
Papers overview Semantic Scholar uses AI to extract papers important to this topic. The synthesis of ribosomal subunits in eukaryotes requires the interplay of numerous maturation and assembly factors (AFs) that… Expand Linezolid can be considered as the first member of the class of oxazolidinone antibiotics. The compound is a synthetic antibiotic… Expand Methylation of nucleotides in ribosomal RNAs (rRNAs) is a ubiquitous feature that occurs in all living organisms. Identification… Expand Sequencing of the 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Specialized 16S rRNA databases… Expand Intercellular communications play a major role in tissue homeostasis.
llrs 4, 455 1 gold badge 11 silver badges 37 bronze badges answered Jan 5 '18 at 5:49 3 Not the answer you're looking for? Browse other questions tagged rna-seq scrnaseq rna ribosomal or ask your own question.
Created by George Rice, Montana State University Ribosomes are the universal ribonucleoprotein particles that translate the genetic code into proteins. They are built of two subunits that associate upon initiation of protein synthesis. Typical eubacterial ribosomes (70S) consist of 57 different molecules (3 rRNAs and 54 proteins) and can dissociate into a small (30S) and a large subunit (50S). The small subunit is responsible for the formation of the initiation complex, performs the decoding of the genetic information, and controls the fidelity of codon-anticodon interactions. The large subunit catalyzes the peptide bond formation and provides the path for the nascent polypeptide chain. The section (or gene) that codes for ribosomal RNA in a cell is the 16S rRNA gene (or rDNA gene). Every cell has a 16S rRNA gene as the ribosomal RNA (rRNA) is an integral part of the ribosome, which is responsible for making cellular proteins. This gene is only about 1550 bp in length in prokaryotes and every cell has from one to more than 25 copies of this gene.
This large precursor RNA is then cleaved to make the smaller mature ribosomal RNAs. This is one of the problem cases when one is attempting to define a gene [ What Is a Gene? ]. Bacterial cells need a lot of ribosomal RNA so they usually have multiple copies of the ribosomal RNA operon ( rrn). In E. coli for example, there are usually seven different rrn operons called rrnA, rrnB, etc. In bacterial genomes the operons are located in different parts of the genome—they are unlinked. (By contrast, in eukaryotic genomes they cluster in large tandem arrays. ) The example shown above is the rrnC operon in E. coli. The rectangular boxes represent regions that are transcribed into the large RNA precursor. Open boxes are pieces at the ends that are removed by direct cleavage. The purple boxes are internal regions that removed by making two cuts, one on either side. In this operon there are four transfer RNA genes (tRNA) embedded in the transcriptional unit. These are processed as described in Transfer RNA: Synthesis.
The 16S rRNA molecule folds itself into a shape that must fit like a puzzle piece with other molecules and consequently, some structural elements must be maintained. Therefore, some sections of the sequence may vary and others may not. Literature The RNA World ( more info) Related Links Introductry illustrations of Translation Translation - animation Teaching Activities Protein translation tool at ExPASy - a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
The large 50S ribosomal subunit contains two rRNA species (the 5S and 23S rRNAs). Bacterial 16S, 23S, and 5S rRNA genes are typically organized as a co-transcribed operon. There may be one or more copies of the operon dispersed in the genome (for example, Escherichia coli has seven). Archaea contains either a single rDNA operon or multiple copies of the operon. The 3' end of the 16S rRNA (in a ribosome) binds to a sequence on the 5' end of mRNA called the Shine-Dalgarno sequence. Eukaryotes In contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats; in humans approximately 300–400 rDNA repeats are present in five clusters (on chromosomes 13, 14, 15, 21 and 22). The 18S rRNA in most eukaryotes is in the small ribosomal subunit, and the large subunit contains three rRNA species (the 5S, 5. 8S and 28S rRNAs). Mammalian cells have 2 mitochondrial (12S and 16S) rRNA molecules and 4 types of cytoplasmic rRNA (28S, 5. 8S, 5S (large ribosome subunit) and 18S (small subunit)).
Uploaded by Alejandra Beltrán 0% found this document useful (0 votes) 20 views 7 pages Description: Ribosomal RNA Date uploaded Feb 14, 2016 Copyright © © All Rights Reserved Available Formats PDF, TXT or read online from Scribd Share this document Did you find this document useful? Is this content inappropriate? Report this Document