Long non-coding transcripts

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Unknown (1409)
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Arabidopsis thaliana (28)
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Sinorhizobium meliloti (2)
Thermococcus kodakarensis KOD1 (2)
Pyrococcus abyssi (2)
Iridovirus (1)
Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (1)

Organisms

Homo sapiens (248)
Mus musculus (102)
Drosophila melanogaster (12)
Arabidopsis thaliana (11)
Saccharomyces cerevisiae (9)
Schizosaccharomyces pombe (8)
Rattus norvegicus (7)
Gallus gallus (6)
Sus scrofa (5)
Danio rerio (4)
Caenorhabditis elegans (3)
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Oryza sativa (3)
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Leishmania braziliensis (1)
Nostoc sp. PCC 7120 = FACHB-418 (1)
Kryptolebias marmoratus (1)
Monodelphis domestica (1)
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Toxoplasma gondii VEG (1)
572307 (1)

Repository

ENA (564)
biostudies-arrayexpress (508)
geo (417)
pride (37)
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Disease

Not Available (2)
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Facioscapulohumeral muscular dystrophy (1)
Mixed disorder as reaction to stress (1)
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Cancer (1)
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Colon cancer (1)

Technology Type

Mass Spectrometry (37)
Shotgun proteomics (22)
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Bottom-up proteomics (3)
Data-dependent acquisition (2)
Illumina HiSeq 2000 (1)
Proteogenomics (1)
RNA mass spectrometry (1)
Gel-based experiment (1)

Instrument Platform

Illumina HiSeq 2000 (21)
NextSeq 500 (14)
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Illumina NovaSeq 6000 (4)
454 GS FLX+ (3)
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Infors HT Multitron shaker (2)
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Small RNA Sample Prep Kit v1.5 (1)
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Ion Torrent S5 XL (1)

Publication Date

2014 (166)
2015 (107)
2016 (72)
2013 (68)
2012 (65)
2023 (50)
2011 (49)
2010 (49)
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2018 (42)
2020 (41)
2017 (38)
2024 (37)
2022 (37)
2019 (34)
2026 (34)
2025 (26)
2009 (16)
2008 (13)
2007 (9)
2006 (4)
2005 (2)

UNIPROT ID/AC

Q7ZVT2_DANRE (15)
F6NP87_DANRE (15)
7955.ENSDARP00000111175 (15)
Q6GQM1_DANRE (15)
F1QSE1_DANRE (15)
7955.ENSDARP00000107930 (15)
7955.ENSDARP00000111194 (15)
7955.ENSDARP00000107946 (15)
Q7T334_DANRE (15)
Q6DHI9_DANRE (15)
7955.ENSDARP00000106634 (15)
A2BHA3_DANRE (15)
Q6NZZ2_DANRE (15)
A0A0R4IK21_DANRE (15)
F1QK60_DANRE (15)
7955.ENSDARP00000100434 (15)
E7F5A4_DANRE (15)
Q6IQX2_DANRE (15)
Q6GQM9_DANRE (15)
Q5BJ11_DANRE (15)
RS7_DANRE (15)
Q7T3G2_DANRE (15)
Q8JHI0_DANRE (15)
Q6PC80_DANRE (15)
Q803W9_DANRE (15)
Q803M8_DANRE (15)
Q6DGJ6_DANRE (15)
F1QAU0_DANRE (15)
A0A140LG54_DANRE (15)
B8JIS5_DANRE (15)

ENSEMBL ID

ENSDARP00000125163 (17)
ENSDARP00000123922 (17)
ENSDARP00000116010 (17)
ENSDARP00000097050 (17)
ENSDARP00000087462 (17)
ENSDARP00000061164 (17)
ENSDARP00000000221 (17)
ENSDARG00000092233 (17)
ENSDARG00000092126 (17)
ENSDARG00000087390 (17)
ENSDARG00000079782 (17)
ENSDARG00000079564 (17)
ENSDARG00000075758 (17)
ENSDARG00000074289 (17)
ENSDARG00000071430 (17)
ENSDARG00000070083 (17)
ENSDARG00000068992 (17)
ENSDARG00000063908 (17)
ENSDARG00000058371 (17)
ENSDARG00000058358 (17)
ENSDARG00000056248 (17)
ENSDARG00000055996 (17)
ENSDARG00000055649 (17)
ENSDARG00000051783 (17)
ENSDARG00000046106 (17)
ENSDARG00000045180 (17)
ENSDARG00000045143 (17)
ENSDARG00000045014 (17)
ENSDARG00000044976 (17)
ENSDARG00000044975 (17)

IsPrivate

False (1)

Submitter Keywords

FAIR-AIML (1)
Machine Learning Model (1)

First Public Date

2014 (60)
2023 (51)
2021 (51)
2026 (46)
2024 (44)
2020 (43)
2018 (42)
2017 (42)
2019 (36)
2013 (35)
2022 (32)
2015 (32)
2025 (29)
2016 (20)
2012 (1)

Classification

protozoa (5)
viruses (4)
fungi (1)
bacteria (1)

Modelling Approach

Machine learning (1)

Modification

2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)

Study type

RNA-seq of coding RNA (191)
Transcription profiling by array (161)
RNA-seq of non coding RNA (62)
ChIP-seq (21)
Other (17)
Unknown experiment type (9)
Transcription profiling by tiling array (8)
Transcription profiling by SAGE (6)
Cell line - High-throughput sequencing (4)
Comparative genomic hybridization by array (3)
DNA-seq (3)
RNA-seq of total RNA (3)
Animal - One-color microarray (2)
Capture-C (2)
ATAC-seq (2)
RIP-seq (2)
Animal - Two-color microarray (1)
Human - Methylation microarray (1)
ChIP-chip by tiling array (1)
Human - One-color microarray (1)
Animal - High-throughput sequencing (1)
CLIP-seq (1)
Transcription profiling by RT-PCR (1)
Methylation profiling by array (1)
Genotyping by high throughput sequencing (1)
RNA-seq of coding RNA from single cells (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2021 (185)
2022 (154)
2015 (153)
2014 (147)
2020 (145)
2016 (139)
2019 (125)
2023 (124)
2017 (107)
2018 (105)
2024 (103)
2013 (96)
2025 (80)
2012 (72)
2011 (60)
2010 (58)
2009 (20)
2008 (14)
2007 (12)
2026 (7)
2006 (5)
2005 (4)
2004 (1)
1999 (1)

Lab affiliation

MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, Scotland (UK) (2)
Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy (1)
National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, China (1)
Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (1)
National Taiwan University, Institute of Molecular & Cellular Biology (1)
Max Planck Institute for Biology of Ageing Joseph-Stelzmann-Str. 9b 50931 Cologne, Germany (1)
1.Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland. 2.Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland. 3. Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland. (1)
Biogenouest Proteomics Core Facility IRSET – INSERM U1085 Rennes, France (1)
Department of Biochemical and Biotechnological Sciences, University of Catania, Italy (1)
Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India (1)
VIB center for Medical Biotechnology, VIB, Ghent, Belgium Department of Biomolecular Medicine, Ghent University, Ghent, Belgium (1)
733 N. Broadway Miller Research Building room 527 Johns Hopkins University Baltimore, MD 21205 (1)
Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland. (1)
Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland (1)
Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA;Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA;McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA (1)
Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo, São José dos Campos, SP, Brazil (1)
i3s - Instituto de Investigação e Inovação em Saúde; INEB - Instituto Engenharia Biomédica; ICBAS - Instituto de Ciências Biomédicas Abel Salazar. (1)
Associate Professor, Division of Hematology, Department of Internal Medicine, The Ohio State University Wexner Medical Center (1)
University Regensburg,Department of Biochemistry, geneticsand Microbiology, Chair of Biochemistry I (1)
VIB Center for Medical Biotechnology, VIB, Ghent Department of Biomolecular Medicine, Ghent University, Ghent (1)
Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany (1)
1 German Cancer Consortium of Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany 2 IIIrd Medical Department, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany 3 Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany (1)
IRIC - University of Montreal (1)
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences (1)
Department of Medical BioSciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands. (1)
Institution of hydrobiology，CAS (1)
University of Pennsyvania, Washington University in St. Louis (1)
Cancer Science Institute of Singapore, National University of Singapore (1)
EMBL (1)
Onstott Lab, Department of Geosciences, Princeton University (1)

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Comprehensive 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

RNA 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

Identification of novel long non-coding RNAs in prostate cancers

Long non-coding RNAs show highly tissue and disease specific expression profiles. We analyzed prostate cancer and normal adjacent prostate samples to identify cancer-specific transcripts and found 334 candidates, of which 15 were validated by RT-PCR. 8 Prostate cancer samples from radical prostatect...

ORGANISM(S): Homo sapiens

2015-03-02 | E-GEOD-59745 | biostudies-arrayexpress

Deshpande2019 - 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

Long RNA Seq on Sham vs MI Adult Mouse Heart

We systematically identified, annotated and characterised the mouse long non-coding transcriptome during myocardial infarction, revealing hundreds of novel heart specific lncRNAs with unique functional and regulatory characteristics. 2 conditions, 4 biological replicates per condition

ORGANISM(S): Mus musculus

2014-05-06 | E-GEOD-52313 | biostudies-arrayexpress

Deregulated long non-coding transcripts in M1 and M2 macrophages

PRJNA800663 | ENA

Custom long non-coding RNA capture enhances detection sensitivity in different human sample types.

Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic ...

EGAS00001005418 | EGA

Global identification of growth-related long non-coding RNAs in breast muscle of chicken

Long non-coding RNAs (lncRNAs) can have potential roles in development of tissues and organs. We selected breast muscle of fast-growing White Recessive Rock chicken (WRR) and slow-growing Xing Hua chicken (XH) to identify lncRNA transcripts by LncRNA-Seq. This study identified 21,993 novel lncRNAs. ...

ORGANISM(S): Gallus gallus

2014-06-24 | E-GEOD-58755 | biostudies-arrayexpress

Type I interferon regulates the expression of long non-coding RNAs [RNA-seq]

Interferons (IFNs) are key players in the antiviral response. IFN sensing by the cell activates transcription of IFN-stimulated genes (ISGs) able to induce an antiviral state by affecting viral replication and release. IFN also induces the expression of ISGs that function as negative regulators to l...

ORGANISM(S): Homo sapiens

2015-01-09 | E-GEOD-64795 | biostudies-arrayexpress

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.

Not available

S-EPMC3783192 | biostudies-literature

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