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Organisms

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human gut metagenome (1)
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Organisms

Mus musculus (223)
Homo sapiens (186)
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Arabidopsis thaliana (11)
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bioreactor metagenome (5)
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Repository

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pride (309)
geo (202)
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Technology Type

Mass Spectrometry (309)
Shotgun proteomics (159)
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Affinity purification coupled with mass spectrometry proteomics (34)
Mass spectrometry assay (33)
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SWATH MS (12)
HDMSE (10)
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DiaPASEF (8)
SRM/MRM (6)
NMR spectroscopy (3)
All-ion fragmentation (2)
Immunopeptidomics (2)
ILLUMINA, Illumina HiSeq 4000 (1)
Illumina MiSeq, Illumina HiSeq 2500 (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
MSE (1)
Mass spectrometry imaging (1)
Metaproteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (80)
NextSeq 500 (65)
Illumina HiSeq 2500 (49)
Illumina HiSeq 4000 (35)
Illumina HiSeq 2000 (30)
Illumina HiSeq 3000 (9)
NextSeq 2000 (8)
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C1 Single-Cell Auto Prep System, Fluidigm (2)
Linux computer (2)
Linux Beowulf cluster; AMD Opteron Linux Beowulf cluster; AMD Opteron 6168 (2)
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Illumina HiSeq 1500 (2)
SnakePipes 3.4 (1)
NEBNext Ultra II DNA Library Prep Kit (1)
Qubit 4.0 Fluorometer/ Agilen 5300 Fragment Analyzer (1)
BD FACSAria™ III (1)
ILLUMINA (1)
Analyses performed on a Linux HPC cluster with Intel Xeon CPUs (1)
Agilent 4200 TapeStation; PCR thermal cycler (Applied Biosystems) (1)
Qubit Fluorometer 3.0 (Thermo Fisher Scientific, USA); Agilent 4200 TapeStation (Agilent Technologies, USA) (1)
Covaris sonicator, PCR thermocycler, magnetic rack for SPRI bead clean-up (1)
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Publication Date

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2020 (102)
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2016 (85)
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2019 (71)
2015 (68)
2018 (53)
2014 (44)
2017 (36)
2013 (32)
2012 (25)
2011 (19)
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2006 (3)
2005 (2)
2004 (1)

UNIPROT ID/AC

A0A075B6P5 (1)
A0A087WT59 (1)
A0A087WTX5 (1)
A0A087WYL9 (1)
A0A087X130 (1)
A0A087X1V9 (1)
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O76015 (1)
O95678 (1)
P00746 (1)
P01009 (1)
P01024 (1)

ENSEMBL ID

ENSG00000170477 (1)

CHEBI ID

CHEBI:28044 (14)
CHEBI:28842 (14)
CHEBI:30769 (14)
CHEBI:30915 (13)
CHEBI:17351 (13)
CHEBI:16704 (12)
CHEBI:18237 (12)
CHEBI:16958 (12)
CHEBI:17568 (12)
CHEBI:17822 (11)
CHEBI:18186 (11)
CHEBI:30746 (11)
CHEBI:18211 (11)
CHEBI:15891 (11)
CHEBI:15428 (11)
CHEBI:18012 (11)
CHEBI:16335 (11)
CHEBI:15354 (11)
CHEBI:17992 (10)
CHEBI:26271 (10)
CHEBI:16811 (10)
CHEBI:28790 (10)
CHEBI:27266 (10)
CHEBI:16359 (10)
CHEBI:16865 (10)
CHEBI:16010 (10)
CHEBI:17015 (10)
CHEBI:17203 (10)
CHEBI:16750 (10)
CHEBI:16919 (10)

Metabolite Name

Adenine (20)
Adenosine (18)
Uridine (17)
Inosine (17)
Hypoxanthine (17)
Guanosine (16)
L-Phenylalanine (16)
Choline (14)
L-Tryptophan (14)
L-Tyrosine (14)
Cholic acid (13)
Citric acid (13)
Azelaic acid (13)
Trigonelline (12)
L-Threonine (12)
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L-Histidine (12)
Taurine (12)
L-Proline (12)
N-Acetyl-L-phenylalanine (12)
L-Serine (12)
Thymidine (12)
Benzoic acid (11)
Serotonin (11)
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Pantothenic acid (11)
Sebacic acid (11)
Tyramine (11)
Histamine (11)
Tetradecanedioic acid (11)

First Public Date

2025 (105)
2024 (90)
2026 (89)
2021 (78)
2019 (74)
2022 (71)
2023 (55)
2020 (54)
2018 (38)
2017 (26)
2014 (16)
2015 (14)
2013 (11)
2016 (8)

Modelling Approach

Constraint-based model (1)

Study status

Recruiting (3)
Not yet recruiting (3)
Completed (3)
Active, not recruiting (1)
Not provided (1)

Lab affiliation

Professor, Deputy Head of Centre Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen, DENMARK (7)
Associate Professor of Genetics Stanford University USA (5)
School of Pharmacy, Sungkyunkwan University, South Korea (5)
Memorial Sloan Kettering Cancer Center (3)
University of Copenhagen Department of Biomedical Sciences Blegdamsvej 3B København N, DK-2200 (3)
Center for Neuroscience and Cell Biology (2)
Chemical and Biological Engineering, Hong Kong University of Science and Technology (HKUST) (2)
DIVAS, University of Milan (2)
Department of Immunology, University of Oslo, Norway (2)
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands (2)
Department of Pharmacology University of North Carolina - Chapel Hill Chapel Hill, NC 27599 (2)
EDyP (2)
Faculty of Pharmacy, Hubei University of Chinese Medicine (2)
German Cancer Reseach Center (DKFZ) (2)
Institute for Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489 Greifswald, Germany (2)
International Institute of Molecular and Cell Biology, Laboratory of RNA-Protein Interactions - Dioscuri Centre, Warsaw, Poland (2)
MS Omics, Biohub Chicago, USA (2)
Massachusetts Institute of Technology (2)
Professor, Microbiology, Immunology, and Pathology Mycobacteria Research Laboratories Scientific Director, Rocky Mountain Regional Biocontainment Laboratory Editor-in-chief, BMC Mycobacteria (2)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (2)
Proteomics Unit Navarrabiomed, Pamplona, Spain (2)
Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, Skopje, Krste Misirkov 2, 1000 Skopje, Republic of North Macedonia (2)
Robert W. Holley Center for Agriculture and Health United States Department of Agriculture Agricultural Research Service (2)
School of Biological Sciences, Te Herenga Waka Victoria University of Wellington, New Zealand (2)
1. Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel 2. Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel (1)
1.Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA 2.Department of Microbiology, Harvard Medical School, Boston, MA, USA 3.Howard Hughes Medical Institute, Boston, MA, USA (1)
1UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia (1)
Aalborg University (1)
Associate Professor Department of Biological Sciences University of Denver (1)
Associate Professor at University of Campinas, Sao Paulo-Brazil (UNICAMP-SP. (1)

Keyword

Costeffectiveness (1)
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Low rectal cancer (1)
Minimally invasive colorectal surgery (1)
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TEM (1)
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Colonoscopy (1)

IsPrivate

False (1)

Classification

viruses (9)
bacteria (6)
fungi (2)
protozoa (2)

Modification

15.994915 (1)
4x(2)H labeled dimethylated L-lysine (1)
57.021464 (1)

Study type

RNA-seq of coding RNA (271)
Transcription profiling by array (116)
ChIP-seq (44)
RNA-seq of coding RNA from single cells (32)
RNA-seq of total RNA (19)
Animal - High-throughput sequencing (14)
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DNA-seq (9)
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Baseline (5)
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Unknown experiment type (1)
Differential (1)
Cell line - One-color microarray (1)
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Release Date

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2005 (3)
2000 (2)
2004 (1)
2003 (1)
2001 (1)

Location

China (3)
Australia (2)
Japan (2)
New Zealand (1)
Egypt (1)
Italy (1)
Netherlands (1)

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Annotating Low Abundance and Transient RNAs in Yeast using Ultra High-throughput Sequencing

Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays and Ultra High-throughput Sequencing Reveals New Transcripts that are not Conserved Across Closely Related Yeast Species A complete description of the transcriptome of an organism is crucial for a comprehensive understand...

ORGANISM(S): Saccharomyces cerevisiae

2008-12-18 | E-GEOD-11801 | biostudies-arrayexpress

Comprehensive analysis of RNA-seq kits for standard, low and ultra-low quantity samples

PRJNA510978 | ENA

Cell-free DNA methylome profiling by MBD-seq with ultra-low input

PRJNA677900 | ENA

Improved sensitivity of ultra-low flow LC-MS-based proteomic profiling of limited samples using monolithic capillary columns and FAIMS technology

In this work, we pioneered a combination of ultra-low flow (ULF) high-efficiency ultra-narrow bore monolithic LC columns coupled to MS via a high-field asymmetric waveform ion mobility spectrometry (FAIMS) interface to evaluate the potential applicability for high sensitivity, robust and reproducibl...

ORGANISM(S): Homo sapiens (Human)

2021-01-10 | PXD020669 | Pride