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MicroRNAs (miRNAs) are key regulators of gene expression and contribute to a variety of biological processes including cell growth, differentiation, and development. Abnormal microRNA expression has been reported in various diseases including various cancers, cardiovascular disease, and neurological disorders. Therefore microRNAs are considered to be promising diagnostic and therapeutic candidates for the treatment of human disease.

The miRBase sequence database, is the public repository for all known microRNAs. Newly discovered microRNAs are routinely added and it has grown rapidly with approximately >10,000 entries to date. Despite this rapid growth, many miRNAs have not yet been validated, and many believe there are numerous microRNAs yet to be identified. A lack of a full complement of miRNAs has imposed limitations on recognizing their important roles in development and disease.

Now researchers are using the latest in deep sequencing technology along with advanced bioinformatics packages to identify novel microRNAs in various tissue types and species.

• Ryu S, Joshi N, McDonnell K, Woo J, Choi H, et al. (2011) Discovery of Novel Human Breast Cancer MicroRNAs from Deep Sequencing Data by Analysis of Pri-MicroRNA Secondary Structures. PLoS ONE 6(2), e16403. [article]
• Xie SS, Li XY, Liu T, Cao JH, Zhong Q, Zhao SH. (2011) Discovery of Porcine microRNAs in Multiple Tissues by a Solexa Deep Sequencing Approach. PLoS One 6(1), e16235. [article]
• Creighton CJ, Benham AL, Zhu H, Khan MF, Reid JG, Nagaraja AK, Fountain MD, Dziadek O, Han D, Ma L, Kim J, Hawkins SM, Anderson ML, Matzuk MM, Gunaratne PH. (2010) Discovery of novel microRNAs in female reproductive tract using next generation sequencing. PLoS One 5(3), e9637. [article]
• Huang QX, Cheng XY, Mao ZC, Wang YS, Zhao LL, Yan X, Ferris VR, Xu RM, Xie BY. (2010) MicroRNA discovery and analysis of pinewood nematode (Bursaphelenchus xylophilus) by deep sequencing. PLoS One 5(10), e13271. [article]
• Song C, Wang C, Zhang C, Korir NK, Yu H, Ma Z, Fang J. (2010) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11, 431. [article]
• Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ. (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 10, 3. [article]

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• SEQanswers – RNA Sequencing

  • RNAseq (SOLiD) from 18 - 200 nt June 18, 2013
    We are interested in small non-coding RNAs. Whomever you ask about the size range of small RNAs, you get a different answer. ;) Lets assume, small... […]
    GenomicIBK
  • Unmapped ratio very high on mouse genome June 17, 2013
    Hi, My problem regards RNA-Seq data. I've downloaded public data (SAGE libs w/ 6 different samples from mouse liver ) to analyse using ArrayStudio.... […]
    le.nono
  • RNASeq: Read length different from expected June 17, 2013
    Hello all, I have received paired-end reads for 40 samples. The reads are supposed to be 100bp per end. Instead, 20 of my samples are 101bp per... […]
    gogodidi
  • How to install xgawk June 16, 2013
    Hi, This is Shrujan, i have a problem while running RNA Sequencing QC. It shows an error that xgawk is not found. So please help me installing... […]
    shrujan
  • RNA Sequencing QC Error while using with Sequence_QC.sh file June 15, 2013
    Hi, This is Shrujan kumar Madadha, I had an error while running QC for Drosophila Yukuba fastq RNA file using Sequence_QC.sh file of FASTX... […]
    shrujan
  • Cuffmerge related query June 12, 2013
    I have a query regarding what samples should be merged using cuffmerge, when you have multiple phenotypes (each with replicates). Lets say my mouse... […]
    ParthavJailwala

• Biostar – RNA-Seq

  • Normalising tag count to RPKM
    Hi! I was wondering if their is a way to normalise the number of reads in a region and the RPKM of the nearest gene to that region, so that a correlation could be computed. Like the following data shows number of tags in first column and RPKM in second column Tags RPKM 15 0.14619 11 0 203 0.2259 129 10.701 300 7.0772 122 2.3234 346 10.666 77 3.117 201 16.749 […]
  • a simple question on RNA-Seq terminology
    This question may be very simple and basic, but I just need to confirm that I understand the differences among those terminologies in the RNA-Seq context. Suppose I have a sample called SLR, and it is sequenced on 5 lanes, so I have (among other output files) BAM files like L1_SLR, L2_SLR, L3_SLR, L5_SLR and L7_SLR.bam. Here, the letter "L" denotes […]
  • FInding regions of interest with minimum coverage
    Hi, I have a bam file of all my accepted hits (tophat output) and an gtf file with my genes of interest for which I am trying to find potential antisense transcripts. I would like to create a list - preferably one that can be visualized in a genome browser - that shows all genes that have antisense reads in the accepted hits.bam file provided that there are […]
  • How to remove the intronic reads before counting
    I got RNASeq data in several samples. I checked the FastQC, seems the read quality are good (Hiseq 2000). But the problem is many reads are mapped to intronic region, and the regions have no any reference exons there (Refseq, ensembl, gencode). We don't know what they are. We guess the problem happend in library preparation, the concentration was low. N […]
  • Which strand of the mRNA molecule does the sequencer output as a "read"?
    In Illumina Stranded RNA-Seq (using the dUTP method), do the final reads in the fastq files correspond to the initial molecule (that was transcribed), or to the reverse complement of the molecule? C […]
  • RNA-Seq: novel transcripts found. What next?
    If I were use cufflinks in de novo mode to find transcripts or genes in my data that did not align to known transcripts from UCSC or Ensembl, I wouldn't know what to do downstream of this. How would one go about confirming that these are indeed novel? What sort of validation steps would one take (computational or non-computational), what in-depth inform […]