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ModelsDeshpande2019 - Random Forest model to predict long non-coding RNAs from coding RNAs in Zea Mays plant transcriptomic data
This is a Random Forest algorithm-based machine learning model to predict lncRNAs from coding mRNAs in plant transcriptomic data. The model assigns 1 for coding sequences and 2 for long non-coding sequences. The prediction is performed using a combination of Open Reading Frame (ORF) based, Sequence-...
2024-12-09 | BIOMD0000001067 | BioModels
Machine Learning Model FAIR-AIML 
TranscriptomicsGlobal identification and characterization of intermediate-size non-coding RNAs in Oryza sativa
In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown function...
ORGANISM(S): Oryza sativa Japonica Group 
2012-07-27 | E-GEOD-39695 | biostudies-arrayexpress
ProteomicsA novel protein coding potential of long intergenic non-coding RNAs (lincRNAs) in the kinetoplastid protozoan parasite Leishmania major
Leishmania major is a kinetoplastid protozoan parasite which causes the debilitating infectious disease cutaneous leishmaniasis (CL). This disease results in scars and disfiguration of the infected individuals. The L. major genome was the first leishmanial genome to be sequenced in 2005 and this stu...
ORGANISM(S): Leishmania major 
2016-05-11 | PXD002465 | Pride
Cutaneous leishmaniasis Proteomics Gene annotations Non-coding rna Protozoan parasite 
TranscriptomicsGenomic features and regulatory roles of intermediate-size non-coding RNAs in Arabidopsis
Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biological processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs...
ORGANISM(S): Arabidopsis thaliana 
2014-01-20 | E-GEOD-44235 | biostudies-arrayexpress
TranscriptomicsNext generation sequencing of small RNAs isolated from exosomes in human semen
Preparation of exosomes isolated from semen contain a substantial amount of RNA, mostly from 20 to 100 nucleotides in length. We sequenced separately 20-40 and 40-100 nucleotide fractions of RNA from exosomes isolated from semenal fluid from six healthy donors. We found various classes of small non...
ORGANISM(S): Homo sapiens 
2014-06-04 | E-GEOD-56076 | biostudies-arrayexpress
TranscriptomicsRNA at 92 M-BM-0C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.
The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transc...
ORGANISM(S): Pyrococcus abyssi 
2014-05-31 | E-GEOD-58131 | biostudies-arrayexpress
TranscriptomicsGenome-wide profiling of miRNAs and other small non-coding RNAs in the Verticillium dahliae inoculated cotton roots
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are short (19–25 nucleotides) non-coding RNA molecules that have large-scale regulatory effects on development and on stress responses in plants.The objective of this study is to investigate the transcriptional profile of miRNAs and other smal...
ORGANISM(S): Gossypium hirsutum 
2011-04-29 | E-GEOD-28236 | biostudies-arrayexpress
ProteomicsComprehensive Identification of Soybean Long Non-coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts
Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from variou...
ORGANISM(S): Glycine max 
2020-01-09 | PXD014553 | Pride
Long non-coding rna Proteomics Soybean Small peptide Transcriptomics 
ProteomicsThe transient Spt4-Spt5 complex as an upstream regulator of non-coding RNAs during development
The Spt4-Spt5 complex is conserved and essential RNA polymerase elongation factor. To investigate the role of the Spt4-Spt5 complex in non-coding transcription during development, we used the unicellular model Paramecium tetraurelia. In this organism harboring both germline (micronucleus - MIC) and ...
ORGANISM(S): Paramecium tetraurelia 
2022-04-27 | PXD027748 | Pride
Interactomics Spt4 Meiosis 
TranscriptomicsNon-coding RNA tiling array in rice
The 1 Mb tiling array was used to represent the 10.0 Mb to 11.0 Mb region of japonica rice Chromosome 10. A tile path was designed with 36-mer probes at a step of 5 nt. All 388,994 probes were retained and synthesized into a single array. This array was hybridized to the cDNA target used for the ful...
ORGANISM(S): Oryza sativa 
2010-06-11 | E-GEOD-6922 | biostudies-arrayexpress
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