Cage - OmicsDI

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Unknown (4262)
Genomics (1020)
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Organisms

Mus musculus (410)
Homo sapiens (173)
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mouse gut metagenome (4)
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Mus musculus musculus x M. m. domesticus (1)

Organisms

Mus musculus (240)
Homo sapiens (185)
Rattus norvegicus (71)
Drosophila melanogaster (14)
Arabidopsis thaliana (14)
Gallus gallus (9)
mouse gut metagenome (8)
Saccharomyces cerevisiae (8)
Macaca mulatta (4)
feces metagenome (4)
Danio rerio (4)
Halenospora varia (3)
Lonchura striata (3)
Photobacterium damselae subsp. damselae (3)
Schizosaccharomyces pombe (3)
Salmo salar (3)
Sus scrofa (3)
Chaetomium sp. MPI-CAGE-AT-0009 (2)
Dendryphion nanum (2)
Thelonectria olida (2)
Dactylonectria estremocensis (2)
Fusarium flagelliforme (2)
Microdochium trichocladiopsis (2)
Stachybotrys elegans (2)
Linnemannia elongata (2)
Ilyonectria sp. MPI-CAGE-AT-0026 (2)
Seriola lalandi (2)
Fusarium redolens (2)
Oplegnathus fasciatus (2)
Dactylonectria macrodidyma (2)

Repository

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biostudies-arrayexpress (672)
geo (271)
pride (75)
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Normal (11)
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Technology Type

Mass Spectrometry (76)
Mass spectrometry (52)
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Bottom-up proteomics (12)
NMR spectroscopy (11)
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Data-independent acquisition (7)
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Top-down proteomics (6)
Chemical cross-linking coupled with mass spectrometry proteomics (3)
DiaPASEF (3)
Gel-based experiment (3)
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NMR spectroscopy assay (1)
ESI (1)
HDMSE (1)
SWATH MS (1)

Instrument Platform

Illumina HiSeq 2500 (19)
Illumina NovaSeq 6000 (17)
Illumina HiSeq 2000 (12)
NextSeq 500 (12)
Scanning hardware (11)
Illumina HiSeq 4000 (9)
Illumina MiSeq (8)
454 GS FLX+ (3)
Helicos HeliScope (3)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
GenePix 4000B [Axon Instruments] (2)
Illumina Genome Analyzer II (2)
NextSeq 2000 (2)
MinION (2)
GeneTitan MultiChannel System (1)
GeneChip Clariom S mouse array cartridge and Affymetrix GeneTitan MultiChannel System (1)
GeneChip Pico Kit (Affymetrix/ThermoFisher) (1)
ReliaPrep RNA Miniprep System (Promega) (1)
Adipocyte Progenitor Isolation Kit (Miltenyi Biotec) (1)
Chromium Next GEM Chip G (1)
10X v3 (1)
Described in protocol (1)
Sequel II (1)
Nanopore sequencing (1)
AB 3730xL Genetic Analyzer (1)
Maxwell® 16 AS2000 (1)
ScanArray Lite [Perkin Elmer] (1)
Qiagen (1)
Affymetrix GeneChip Scanner 3000 7G (1)
Agilent Technologies G2505B scanner (1)

Publication Date

2014 (106)
2015 (76)
2012 (70)
2010 (64)
2013 (62)
2011 (60)
2023 (59)
2024 (59)
2025 (57)
2016 (57)
2022 (45)
2021 (45)
2026 (44)
2008 (43)
2020 (38)
2018 (38)
2006 (38)
2009 (36)
2019 (34)
2017 (32)
2007 (29)
2005 (13)
2004 (5)

UNIPROT ID/AC

Q30201 (1)
Q9UP52 (1)
P09601 (1)
P81172 (1)
P02786 (1)
P02787 (1)
Q9NP59 (1)
P21399 (1)

CHEBI ID

CHEBI:16919 (26)
CHEBI:17596 (24)
CHEBI:15741 (23)
CHEBI:17568 (23)
CHEBI:17368 (23)
CHEBI:15428 (22)
CHEBI:15891 (22)
CHEBI:28044 (21)
CHEBI:16704 (21)
CHEBI:15354 (21)
CHEBI:27266 (20)
CHEBI:30769 (20)
CHEBI:18012 (19)
CHEBI:27897 (19)
CHEBI:16811 (18)
CHEBI:16708 (18)
CHEBI:17754 (18)
CHEBI:16737 (18)
CHEBI:25094 (17)
CHEBI:18237 (17)
CHEBI:18186 (17)
CHEBI:24898 (17)
CHEBI:25017 (17)
CHEBI:17268 (17)
CHEBI:32816 (17)
CHEBI:78320 (17)
CHEBI:17154 (16)
CHEBI:82594 (2)
CHEBI:192761 (2)
CHEBI:29033 (2)

Metabolite Name

Uracil (13)
Inosine (13)
Phenylalanine (12)
Taurine (12)
Inosine (11)
Uracil (11)
Glycine (11)
Valine (11)
Choline (11)
Isoleucine (11)
Creatine (11)
Hypoxanthine (11)
Uridine (10)
Lysine (10)
Glycerol (10)
Cytosine (10)
Phenylalanine (10)
Leucine (9)
Glycine (9)
Taurine (9)
Hypoxanthine (9)
AMP (9)
Methionine (9)
Creatine (9)
Tyrosine (9)
Fumarate (9)
Acetate (8)
Ribose (8)
Proline (8)
Guanosine (8)

First Public Date

2024 (118)
2014 (115)
2025 (102)
2026 (96)
2023 (80)
2018 (68)
2020 (65)
2022 (64)
2021 (60)
2019 (50)
2017 (49)
2015 (31)
2016 (27)
2013 (18)
2012 (2)

Modelling Approach

Differential equation model (2)
Constraint-based model (1)

Study status

Not yet recruiting (1)

Lab affiliation

College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University (2)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (2)
"Philip Morris R&D, Neuchatel, Switzerland" (1)
Associate professor, Department of Biomedical laboratory sciences and chemical engineering, Bergen University College, Bergen, Norway. (1)
Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY (1)
Center for Reproductive Evolution Syracuse University (1)
Centre for Inflammatory Diseases, Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia. (1)
Centre for Proteome Research, Department of Biochemistry, University of Liverpool, UK (1)
Centre for Proteome Research, University of Liverpool (1)
Centre for medicines discovery, University of Oxford (1)
Department Molekulare Systembiologie Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Permoserstraße 15 | 04318 Leipzig Telefon +49 341 235 4767 | Fax +49 341 235 450823 (1)
Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC29425, USA (1)
Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA (1)
Department of Chemical and Biological Engineering, Tufts University; Medford, MA 02155, USA Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843, USA, Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas Health Science Center, Texas A&M University; Bryan, TX, USA (1)
Department of Chemistry University of Nebraska-Lincoln Lincoln, NE 68588 USA (1)
Department of Epidemiology, College of Public Health, Zhengzhou University (1)
Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic (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)
Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Sciences University, Portland, Oregon, USA (1)
Department of Orthopaedics, The Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong District, Chongqing 400010, China (1)
Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States (1)
Department of Pediatrics, Group on Molecular and Cell Biology of Lipids 328 Heritage Medical Research Centre, University of Alberta, Edmonton, Alberta, Canada Phone: (780) 492-2963 Fax: (780) 492-3383 (fax) (1)
Department of Pharmacology, Harbin Medical University, Heilongjiang 163319, China (1)
Department of Plants and Crops, Ghent University, Belgium (1)
Department of Veterinary Sciences Comparative Perinatal Development (CoPeD) University of Antwerp Belgium (1)
Dept of Neurology University Hospital RWTH Aachen Pauwelsstrasse 30 52074 Aachen Germany (1)
Developmental Genetics Unit, Institute of Biology, University of Kassel, Germany (1)
Division of Biology and Biological Engineering, California Institute of Technology,USA (1)
Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (1)
Division of Neurobiology The Roslin Institute Royal (Dick) School of Veterinary Studies College of Medicine and Veterinary Medicine University of Edinburgh Easter Bush Midlothian EH25 9RG SCOTLAND, UK (1)

IsPrivate

False (3)

Submitter Keywords

Not Peer Reviewed (1)

Classification

fungi (11)
bacteria (4)
viruses (2)
protozoa (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (438)
RNA-seq of coding RNA (103)
ChIP-seq (21)
Transcription profiling by tiling array (14)
RNA-seq of non coding RNA (14)
DNA-seq (10)
Methylation profiling by array (10)
RNA-seq of coding RNA from single cells (9)
RNA-seq of total RNA (8)
Methylation profiling by high throughput sequencing (6)
Animal - High-throughput sequencing (5)
Comparative genomic hybridization by array (5)
Other (5)
Unknown experiment type (4)
Animal - One-color microarray (3)
One-color microarray (2)
Cell line - High-throughput sequencing (2)
ChIP-chip by array (2)
Genotyping by array (2)
MicroRNA profiling by array (2)
ChIP-chip by tiling array (1)
High-throughput sequencing (1)
Bisulfite-seq (1)
RIP-seq (1)
Genotyping by high throughput sequencing (1)
Interventional (1)

Release Date

2022 (490)
2023 (466)
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2024 (384)
2020 (366)
2019 (290)
2018 (254)
2016 (242)
2017 (235)
2014 (213)
2015 (211)
2013 (139)
2012 (139)
2011 (128)
2010 (125)
2009 (80)
2008 (73)
2026 (65)
2006 (55)
2007 (44)
2005 (27)
2004 (8)
2002 (8)
2001 (8)
2003 (6)
2000 (2)
1999 (2)
1998 (1)
1996 (1)

Location

India (1)

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CAGE experiment of S. Cerevisiae strain CEN.PK113-7D in four different chemostat conditions

The CAGE experiment was performed in four different chemostat conditions to assess if and how much the Transcription start site landscape changes in the industrial relevant S. Cerevisiae strain CEN.PK113-7D in different conditions. CAGE was also used to obtain accurate TSS annotations for each expre...

ORGANISM(S): Saccharomyces cerevisiae

2019-01-03 | E-MTAB-6650 | biostudies-arrayexpress

SLIC-CAGE (Super-Low Input Carrier-CAGE) development: comparison with Saccharomyces cerevisiae nAnTi-CAGE and nanoCAGE libraries and validation of SLIC-CAGE on Mus musculus total RNA

We developed SLIC-CAGE (Super-Low Input Carrier-CAGE) approach to capture 5'end of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. The dramatic increase in sensitivity compared to existing CAGE methods is achieved by specially designed, selectively degradable carrier RNA. We t...

ORGANISM(S): Saccharomyces cerevisiae S288C

2018-10-25 | E-MTAB-6519 | biostudies-arrayexpress

SLIC-CAGE (Super-Low Input Carrier-CAGE) application on mouse primordial germ cells isolated from embryonic day E11.5

ORGANISM(S): Mus musculus

2018-10-25 | E-MTAB-7056 | biostudies-arrayexpress

SLIC-CAGE of paired-end sequencing data in mouse islets

Super-Low Input Carrier Cap Analysis of Gene Expression (SLIC-CAGE) to identify transcription start sites (TSS) and existing genome-wide maps of islet histone marks to characterise the contribution of transcriptional regulation of LKB1-mediated control of gene expression in mouse β-cells. SLIC-CAGE ...

ORGANISM(S): Mus musculus

2024-09-19 | E-MTAB-14336 | biostudies-arrayexpress

Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [CAGE-seq]

Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gen...

ORGANISM(S): Homo sapiens

2015-05-21 | E-GEOD-61264 | biostudies-arrayexpress

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Sequencing of 5' ends of RNA molecules from control and exosome-depleted HeLa-S3 cells. CAGE library construction from RNA extracted from control and exosome-depleted cells.

ORGANISM(S): Homo sapiens

2014-07-02 | E-GEOD-58991 | biostudies-arrayexpress

Regional Differences in gene expression and promoter usage in aged human brains

Cap analysis of gene expression (CAGE) and massive parallel sequencing were used to profile the promoterome of aged human brains from five regions, namely: caudate, frontal cortex, hippocampus, putamen and temporal cortex. 25 RNA libraries from post-mortem brain tissue (five caudate, five frontal, ...

ORGANISM(S): Homo sapiens

2013-01-15 | E-GEOD-43472 | biostudies-arrayexpress

Ilyonectria sp. MPI-CAGE-AT-0026

Ilyonectria sp. MPI-CAGE-AT-0026 Transcriptome - Ily_026_T

PRJNA444682 | ENA

Chaetomium sp. MPI-CAGE-AT-0009

Chaetomium sp. MPI-CAGE-AT-0009 Transcriptome - Cha_009_T

PRJNA534635 | ENA

CAGE-seq of human colon cancer cell line (HCT116) upon TBX3 overexpression

The Wnt/β-catenin signaling pathway plays crucial roles in nearly all parts of embryonic development and adult stem cell homeostasis. Its aberrant activation has been linked to many diseases such as developmental irregularities and various severe forms of cancer, with colorectal cancer (CRC) as a pr...

ORGANISM(S): Homo sapiens

2024-01-01 | E-MTAB-13647 | biostudies-arrayexpress

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