Pol E E - OmicsDI

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Transcriptomics (4575)
Unknown (1492)
Genomics (1211)
Proteomics (97)
Other (6)
Metabolomics (3)
Multiomics (2)
Models (1)
Methylation profiling (1)

Organisms

Homo sapiens (1558)
Mus musculus (1111)
Drosophila melanogaster (375)
Caenorhabditis elegans (352)
Arabidopsis thaliana (277)
Saccharomyces cerevisiae (277)
Rattus norvegicus (112)
Escherichia coli (112)
Schizosaccharomyces pombe (79)
Streptococcus pneumoniae D39 (58)
Candida albicans (53)
Escherichia coli str. K-12 substr. MG1655 (35)
Bacillus subtilis (30)
Danio rerio (29)
Gallus gallus (28)
Bos taurus (27)
Sus scrofa (27)
Oncorhynchus mykiss (25)
Escherichia coli K-12 (22)
Macaca mulatta (21)
Plasmodium falciparum (21)
Staphylococcus aureus (20)
Mycobacterium tuberculosis (17)
Streptococcus pneumoniae (17)
Salmonella enterica subsp. enterica serovar Typhimurium (16)
Pseudomonas putida (16)
Triticum aestivum (16)
Thermus thermophilus HB8 (13)
Bacillus subtilis subsp. subtilis str. 168 (13)
Apis mellifera (12)

Organisms

Mus musculus (22)
Drosophila melanogaster (14)
Homo sapiens (10)
Escherichia coli (4)
Glycine max (3)
Caenorhabditis elegans (2)
Arabidopsis thaliana (2)
Schizosaccharomyces pombe (1)
Macaca mulatta (1)

Repository

biostudies-arrayexpress (5701)
ENA (72)
pride (46)
geo (35)
MassIVE (35)
EGA (17)
jPOST (5)
iProX (3)
MetaboLights (3)
ExpressionAtlas (2)
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Tissue

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Blood (2)
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Sciatic nerve (2)
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HEK-293T cell (1)
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Disease

Normal (42)
Breast cancer (7)
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Neuroblastoma (4)
Rheumatoid arthritis (3)
Mitochondrial complex I deficiency (2)
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Lymphoblastic leukemia (1)
Benign nevi (1)
Early-life seizures (1)
Dermal neurofibroma (1)
Hepatomegaly (1)
Epithelioid mesothelioma (1)
Unspecified peripheral T-cell lymphoma (1)
Large cell carcinoma (1)
Invasive pituitary adenoma (1)
Oropharynx squamous-cell carcinoma in DiseaseLocation oropharynx has DiseaseStaging lymph node negative (N0) (1)

Technology Type

Mass Spectrometry (46)
Shotgun proteomics (21)
Affinity purification coupled with mass spectrometry proteomics (14)
Bottom-up proteomics (8)
Gel-based experiment (5)
Chemical cross-linking coupled with mass spectrometry proteomics (4)
Data-dependent acquisition (4)
Mass spectrometry (2)
Mass spectrometry assay (1)
All-ion fragmentation (1)
Data-independent acquisition (1)
Top-down proteomics (1)

Instrument Platform

Illumina HiSeq 2000 (89)
Illumina NovaSeq 6000 (72)
NextSeq 500 (66)
Illumina HiSeq 2500 (49)
Illumina HiSeq 4000 (33)
NextSeq 550 (30)
Illumina MiSeq (28)
Scanning hardware (18)
Illumina Genome Analyzer II (15)
Axon- GenePix4000B (12)
GenePix 4000A [Axon Instruments] (11)
Illumina Genome Analyzer IIx (11)
GenePix 4000B [Axon Instruments] (11)
Affymetrix Fluidics Station 400 (11)
Axon GenePix 4000B scanning hardware (11)
ScanArray 4000 [PerkinElmer] (10)
G2565BA DNA microarray scanner [Agilent] (9)
NextSeq 2000 (9)
Illumina NovaSeq X (8)
HiSeq X Ten (8)
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G2565AA DNA microarray scanner [Agilent] (6)
Illumina HiSeq 1500 (6)
GenePix Personal 4100A [Axon Instruments] (5)
BAS-5000 [FUJIFILM] (5)
Other (5)
ScanArray scanning hardware (4)
Illumina Genome Analyzer (4)
G2500A Hewlett Packard (4)
ScanArray Lite [PerkinElmer] (4)

Publication Date

2010 (839)
2013 (786)
2012 (617)
2011 (615)
2014 (571)
2015 (483)
2008 (336)
2009 (275)
2016 (251)
2007 (185)
2006 (122)
2022 (115)
2005 (98)
2023 (66)
2021 (59)
2004 (58)
2018 (54)
2020 (53)
2025 (52)
2017 (51)
2019 (48)
2024 (46)
2026 (34)
2003 (14)
2002 (1)

CHEBI ID

CHEBI:15428 (2)
CHEBI:16958 (2)
CHEBI:17268 (2)
CHEBI:17368 (2)
CHEBI:18012 (2)
CHEBI:30769 (2)
CHEBI:30805 (2)
CHEBI:32816 (2)
CHEBI:33508 (2)
CHEBI:48430 (2)
CHEBI:1148 (1)
CHEBI:116314 (1)
CHEBI:133172 (1)
CHEBI:139421 (1)
CHEBI:14314 (1)
CHEBI:15356 (1)
CHEBI:15429 (1)
CHEBI:15584 (1)
CHEBI:15603 (1)
CHEBI:15741 (1)
CHEBI:15756 (1)
CHEBI:15824 (1)
CHEBI:15929 (1)
CHEBI:15966 (1)
CHEBI:15978 (1)
CHEBI:16000 (1)
CHEBI:16010 (1)
CHEBI:16015 (1)
CHEBI:16027 (1)
CHEBI:16119 (1)

Metabolite Name

Citric acid (2)
Dodecanoic acid (2)
Fumaric acid (2)
Glyceric acid (2)
Glycine (2)
Pyroglutamic acid (2)
Pyruvic acid (2)
2-aminobutanoic acid (1)
2-hydroxybutanoic acid (1)
2-oxo-isocaproic acid (1)
3-Methyl-2-oxopentanoic-acid (1)
3-hydroxybutanoic acid (1)
4-Deoxythreonic acid (1)
Alanine (1)
Alpha-Linolenic acid (1)
Alpha-Tocopherol (1)
Ascorbic acid (1)
Asparagine (1)
Aspartic acid (1)
Azelaic acid (1)
Benzoic acid (1)
Beta-Sitosterol (1)
Butyric acid (1)
Campesterol (1)
Citramalic acid (1)
Cysteine (1)
D-2-Hydroxyglutaric acid (1)
D-Arabinose (1)
D-Fructose (1)
D-Glucose (1)

IsPrivate

False (1)

Model Flag

Non Kinetic (1)

First Public Date

2014 (12)
2025 (8)
2023 (8)
2013 (8)
2021 (7)
2026 (6)
2018 (5)
2022 (4)
2017 (3)
2015 (3)
2024 (2)
2020 (2)
2016 (2)
2019 (1)
2012 (1)

Classification

bacteria (4)

Modelling Approach

Constraint-based model (1)

Study type

Transcription profiling by array (2799)
ChIP-seq (1033)
RNA-seq of coding RNA (765)
ChIP-chip by tiling array (200)
RNA-seq of non coding RNA (143)
ChIP-chip by array (110)
Other (100)
Comparative genomic hybridization by array (92)
Unknown experiment type (76)
Methylation profiling by high throughput sequencing (61)
Transcription profiling by tiling array (53)
Methylation profiling by array (34)
RNA-seq of total RNA (25)
RNA-seq of coding RNA from single cells (18)
Cell line - High-throughput sequencing (16)
Animal - High-throughput sequencing (15)
Transcription profiling by RT-PCR (15)
DNA-seq (14)
RIP-seq (13)
Genotyping by array (9)
Proteomic profiling by array (8)
High-throughput sequencing (7)
RNAi profiling by array (7)
Hi-C (7)
MicroRNA profiling by array (6)
Human - High-throughput sequencing (5)
CLIP-seq (4)
GRO-seq (3)
Plant - High-throughput sequencing (3)
ATAC-seq (3)

Release Date

2010 (862)
2013 (839)
2012 (658)
2011 (655)
2014 (646)
2015 (554)
2008 (358)
2016 (321)
2009 (305)
2022 (249)
2007 (201)
2021 (179)
2023 (157)
2020 (156)
2025 (137)
2024 (136)
2006 (135)
2019 (131)
2017 (121)
2018 (118)
2005 (108)
2004 (67)
2026 (41)
2003 (28)
2001 (10)
2002 (8)
1999 (6)
2000 (4)
1998 (3)

Lab affiliation

Medical University of Vienna, Austria (2)
1. Paris-Cité university, Cochin institute CNRS UMR8104, Inserm U1016, 24 rue du faubourg Saint Jacques 75014 Paris, France 2. Department of Endocrinology and National Reference Center for Rare Adrenal Disorders, Cochin hospital, Assistance Publique Hôpitaux de Paris, 24 rue du faubourg Saint Jacques 75014 Paris, France (1)
Biochemistry, University of Colorado, Boulder (1)
CNIO (1)
Department of Biochemistry, University of Oxford, OX13QU, Oxford, United Kingdom (1)
Department of Molecular Biology, Princeton University, USA (1)
Department of Pharmacy, University ‘‘G. d’Annunzio’’ of Chieti-Pescara, Chieti, Italy (1)
Departments of Molecular Neuroscience and Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel (1)
Departments of Molecular Neuroscience and Biomolecular Sciences, Weizmann Institute of Science; Rehovot, Israel. (1)
Dept. of Biological Chemistry, The Hebrew University of Jerusalem (1)
EDyP (1)
Eurecat, Centre Tecnològic de Catalunya. Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT. Reus, Spain (1)
Executive Director Cancer Research Group Leader, Gene Regulation Lab Peter MacCallum Cancer Centre, Parkville VIC 3052, Australia (1)
Faculty of Medecine, University Paris Cité SFR Necker INSERM US24 160 rue de Vaugirard | 75015 Paris (1)
Head of Proteomics (1)
Head of the Curie Institute Mass Spectrometry Platform (1)
IMB, Ackermannweg 4, 55128 Mainz (1)
Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France  (1)
Institute for Microbiology (1)
Institute of Biochemistry and Biophysics, Pol. Acad. Sci. Mass Sepctrometry Laboratory, Head (1)
Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, 38123 Povo (Trento), Italy (1)
Institute of Systems Biology, Seattle, WA. (1)
Integrative Biology and Molecular Genetics Unit (SBIGeM) (1)
Istituto Europeo di Oncologia (IEO) (1)
Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO) Institut Pluridisciplinaire Hubert Curien (IPHC-UMR7178) CNRS - Université de Strasbourg Strasbourg, FRANCE (1)
Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium (1)
Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research,Ghent University, Ghent, Belgium (1)
Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil. Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil. (1)
MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China (1)
Massachusetts Institute of Technology (1)

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Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (I)

Epigenetic control is an important aspect of gene regulation. Despite detailed understanding of many examples, the transcription of non-coding RNA genes by RNA polymerase (pol) III is less well characterized. Here we profile the epigenetic features of pol III target genes throughout the human gen...

ORGANISM(S): Homo sapiens

2010-04-25 | E-GEOD-20040 | biostudies-arrayexpress

Genome-scale reconstruction of the sigma factor network in E. coli

We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for Escherichia coli under different conditions. By obtaining sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-...

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

2014-02-05 | E-GEOD-46737 | biostudies-arrayexpress

RNA Pol III transcriptomes and relationships to Pol II promoters, enhancer-binding factors and chromatin domains

RNA polymerase III transcribes many noncoding RNAs (e.g. tRNAs) important for translational capacity and other functions. Here, we localized RNA polymerase III, alternative TFIIIB complexes (BRF1/2) and TFIIIC in HeLa cells, determining the Pol III transcriptome, defining gene classes, and reveali...

ORGANISM(S): Homo sapiens

2010-04-14 | E-GEOD-20609 | biostudies-arrayexpress

Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (II)

ORGANISM(S): Homo sapiens

2010-04-25 | E-GEOD-20071 | biostudies-arrayexpress

Transcript Analysis of E. coli ATCC 35218 suggest a Role of cranberry Juice in Inhibiting the growth of E. coli

Several different mechanisms have been proposed to explain the possible role of cranberries, cranberry juice, and cranberry extracts in inhibiting bacterial growth. In this report, we showed that Escherichia coli showed slower growth rate in response to the presence of cranberry juice in the growth...

ORGANISM(S): Escherichia coli

2010-11-03 | E-GEOD-12554 | biostudies-arrayexpress

Genome-wide mapping of RNA Pol III binding site (GM12878)

We report the results of chromatin immunoprecipitation following by high-thoughput sequencing (ChIP-Seq) using the GA II platform from Illumina for the human RNA Polymerase III in GM12878 cells. We have also generated a sequenced input DNA datasets for GM12878 cells. For data usage terms and condi...

ORGANISM(S): Homo sapiens

2009-12-31 | E-GEOD-19549 | biostudies-arrayexpress

Genome-wide mapping of RNA Pol III binding site (K562)

We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human RNA Polymerase III in K562 cells. We have also generated a sequenced input DNA datasets for K562 cells. For data usage terms and conditi...

ORGANISM(S): Homo sapiens

2009-12-31 | E-GEOD-19548 | biostudies-arrayexpress

Bdellovibrio bacteriovorus infection of E. coli

The transcriptional response of E. coli being predated by Bdellovibrio bacteriovorus Keywords: Transcriptional analysis 5 biological replicates with 2 technical replicates each of E. coli cells only and E. coli cells 15 minutes post-infection arrays 4 arrays, with samples swapped for each biological...

ORGANISM(S): Escherichia coli

2009-12-08 | E-GEOD-9495 | biostudies-arrayexpress

Transcription profiling of E. coli K12 luxS-dependent gene regulation

The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twen...

ORGANISM(S): Escherichia coli

2008-06-16 | E-GEOD-9582 | biostudies-arrayexpress

Genome-wide mapping of RNA Pol II binding site (GM12878)

We report the results of chromatin immunoprecipitation following by high-thoughput sequencing (ChIP-Seq) using the GA II platform from Illumina for the human RNA Polymerase II in GM12878 cells. We have also generated a sequenced input DNA datasets for GM12878 cells. For data usage terms and condit...

ORGANISM(S): Homo sapiens

2009-12-31 | E-GEOD-19550 | biostudies-arrayexpress

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