Transcription start site

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Unknown (2345)
Genomics (1404)
Transcriptomics (1348)
Other (75)
Proteomics (35)
Methylation profiling (34)
Metabolomics (4)
Genomic (3)

Organisms

Homo sapiens (780)
Mus musculus (565)
Saccharomyces cerevisiae (94)
Drosophila melanogaster (92)
Arabidopsis thaliana (76)
Schizosaccharomyces pombe (50)
Rattus norvegicus (48)
Caenorhabditis elegans (44)
Danio rerio (28)
Rhizobium leguminosarum (18)
Escherichia coli str. K-12 substr. MG1655 (14)
Gallus gallus (13)
Zea mays (12)
Escherichia coli (10)
Sus scrofa (9)
Saccharomyces cerevisiae S288C (7)
Bos taurus (6)
Bacillus subtilis subsp. subtilis str. 168 (5)
Streptococcus pyogenes (5)
Mycobacterium tuberculosis (5)
Plasmodium falciparum (5)
Vitis vinifera (5)
synthetic construct (5)
Macaca mulatta (4)
Canis lupus familiaris (4)
Thermotoga maritima MSB8 (4)
Geobacter sulfurreducens PCA (4)
Prochlorococcus marinus subsp. pastoris str. CCMP1986 (4)
Glycine max (4)
Sinorhizobium meliloti (3)

Organisms

Homo sapiens (284)
Mus musculus (152)
Saccharomyces cerevisiae (47)
Arabidopsis thaliana (27)
Drosophila melanogaster (25)
Schizosaccharomyces pombe (14)
Danio rerio (9)
Rattus norvegicus (8)
Escherichia coli str. K-12 substr. MG1655 (7)
Caenorhabditis elegans (5)
Plasmodium falciparum (3)
Escherichia coli (3)
Toxoplasma gondii RH (2)
Caldicellulosiruptor bescii DSM 6725 (2)
Streptomyces coelicolor A3(2) (2)
Bacillus subtilis (2)
Zea mays (2)
Bombyx mori (2)
Bos taurus (2)
Shigella flexneri 5a str. M90T (1)
Vibrio vulnificus CMCP6 (1)
Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (1)
Paramyxoviridae (1)
Mycobacterium leprae (1)
Giardia lamblia ATCC 50803 (1)
Human immunodeficiency virus (1)
Leptospira interrogans serovar Manilae (1)
Hepatitis B virus (1)
Clostridioides difficile 630 (1)
Brucella melitensis (1)

Repository

biostudies-arrayexpress (1492)
ENA (764)
geo (598)
pride (31)
EGA (10)
dbGaP (3)
MetaboLights (3)
jPOST (2)
MassIVE (2)
GNPS (1)

Tissue

Cell culture (7)
Plant cell (2)
Photosynthetic cell (1)
Platelet (1)
Blood platelet (1)
Bone marrow (1)
Leukocyte (1)
Permanent cell line cell (1)
Oocyte (1)
Cell suspension culture (1)
Breast (1)
Ovary (1)
Embryonic stem cell (1)
Epithelial cell (1)
Leaf (1)
Macrophage (1)
Liver (1)

Disease

Normal (6)
Infiltrating ductal carcinoma (2)
Acute leukemia (2)
Toxicity (1)
Not applicable (1)
Phyllodes tumor (1)
12 DAI with PepMV-EU isolate (1)
No lesions (1)
Challenged with Pieris rapae larvae (1)
Squamous cell carcinoma has accession C0007137 in DiseaseStateDatabase NCI_Thesaurus (1)
Infected with Influenza A/WSN/33 (H1N1) (1)
Apparently healthy (1)
Xenografts with H1299 cell line (1)
Hodgkin lymphoma, mixed cellularity, stage IV (1)
Pancreatic cancer (1)
Primary tumor (1)
Angiogenic chondrosarcoma (1)
Infected (1)
IBDV infected (1)
Head and neck squamous cell carcinoma (1)
Chronic myelogenous leukemia (1)
Infertility (1)
Reference (1)
Colorectal adenocarcinoma (1)
Prostate carcinoma (1)
Carcinoma (1)
Sleeping sickness (1)
Trypanosomiasis (1)
Breast cancer (1)
Type 2 diabetes mellitus (1)

Technology Type

Mass Spectrometry (31)
Shotgun proteomics (13)
Affinity purification coupled with mass spectrometry proteomics (8)
Gel-based experiment (4)
Mass spectrometry (3)
Top-down proteomics (3)
Data-dependent acquisition (3)
Chemical cross-linking coupled with mass spectrometry proteomics (3)
Illumina HiSeq 2000 (2)
Ion Torrent Proton, Illumina MiSeq, NextSeq 550 (1)
Bottom-up proteomics (1)

Instrument Platform

Illumina HiSeq 2500 (38)
NextSeq 500 (36)
Illumina NovaSeq 6000 (34)
Illumina HiSeq 2000 (24)
Illumina HiSeq 4000 (14)
Illumina MiSeq (11)
NextSeq 550 (7)
Illumina Genome Analyzer II (6)
Axon GenePix 4000B scanning hardware (6)
Illumina NovaSeq X (6)
Illumina HiSeq 3000 (5)
NextSeq 2000 (4)
ScanArray 5000 [PerkinElmer] (3)
GenePix 4000B [Axon Instruments] (3)
MinION (3)
Illumina HiSeq 1500 (3)
Sequel II (2)
454 GS FLX+ (2)
ScanArray scanning hardware (2)
Illumina Genome Analyzer (2)
Illumina Genome Analyzer IIx (2)
G2565BA DNA microarray scanner [Agilent] (2)
NA (2)
DNBSEQ-G400 (2)
Illumina HiSeq 1000 (2)
BD Influx Cell Sorter (1)
Using NEBNext Ultra II DNA Library (1)
Thermal cycler, Magnetic stand / beads, Pipettes and tips, Microcentrifuge tubes, Plate shaker (1)
Centrifuge, Pipettes and tips, Agilent 2100 Bioanalyzer, NanoDrop spectrophotometer, Vortex mixer (1)
Liquid nitrogen, -80°C freezer, Surgical tools (scalpels, forceps), Sample tubes / cryovials (1)

Publication Date

2015 (218)
2013 (208)
2012 (196)
2014 (187)
2010 (177)
2011 (169)
2016 (119)
2009 (92)
2025 (81)
2008 (72)
2023 (70)
2021 (68)
2022 (67)
2020 (66)
2024 (60)
2017 (53)
2026 (52)
2019 (52)
2018 (49)
2007 (24)
2006 (22)
2004 (16)
2005 (11)

CHEBI ID

CHEBI:75084 (1)
CHEBI:49311 (1)
CHEBI:177384 (1)
CHEBI:87546 (1)
CHEBI:156100 (1)
CHEBI:28913 (1)
CHEBI:34118 (1)
CHEBI:10357 (1)
CHEBI:82334 (1)
CHEBI:144070 (1)
CHEBI:29452 (1)
CHEBI:88900 (1)
CHEBI:75089 (1)
CHEBI:35986 (1)
CHEBI:16188 (1)
CHEBI:22469 (1)
CHEBI:87510 (1)
CHEBI:75117 (1)
CHEBI:32325 (1)
CHEBI:88528 (1)
CHEBI:17580 (1)
CHEBI:53177 (1)
CHEBI:50462 (1)
CHEBI:75094 (1)
CHEBI:145715 (1)
CHEBI:42394 (1)
CHEBI:43003 (1)
CHEBI:88534 (1)
CHEBI:45919 (1)
CHEBI:32368 (1)

Metabolite Name

Cis-13,16 docosadienoic acid (1)
Unknown_02 (1)
Cis-11,14,17 eicosatrienoic acid (1)
Unknown_01 (1)
Cis-8,11,14 eicosatrienoic acid (1)
Cis, 11,14-eicosadienoic acid (1)
Cis-10-heptadecenoic acid (1)
D25-tridecanoic acid (1)
Linolelaidic acid (1)
Cis-10-pentadecenoic acid (1)
Heneicosanoic acid (1)
Tridecanoic acid (1)
Decanoic acid (1)
Linalool oxB (1)
Linalool oxA (1)
Hotrienol (1)
Geranyl acetone (1)
Trans-Caryophyllene (1)
3-Hexenyl acetate (1)
Beta-Ionone-5-6-epoxide (1)
(E)-2-Pentenal (1)
(E)-2-Octenal (1)
(E)-2-Nonenal (1)
(E)-2-Hexenal (1)
(E)-2-Heptenal (1)
(E,E)-2,4-Heptadienal (1)
Nonanol (1)
3-Hexenol (1)
2-Hexenol (1)
Hexanol (1)

First Public Date

2014 (100)
2020 (64)
2025 (63)
2023 (62)
2013 (60)
2024 (56)
2021 (56)
2022 (53)
2017 (48)
2026 (46)
2015 (44)
2019 (42)
2018 (41)
2016 (28)
2010 (1)

Classification

bacteria (23)
protozoa (9)
viruses (3)
fungi (2)

Modification

N6-dimethyl-L-lysine (1)

Study type

Transcription profiling by array (458)
ChIP-seq (358)
RNA-seq of coding RNA (314)
ChIP-chip by tiling array (54)
Other (47)
Methylation profiling by high throughput sequencing (46)
Methylation profiling by array (44)
RNA-seq of non coding RNA (31)
ChIP-chip by array (29)
Transcription profiling by tiling array (20)
RNA-seq of total RNA (14)
Unknown experiment type (12)
RNA-seq of coding RNA from single cells (11)
Animal - High-throughput sequencing (9)
Comparative genomic hybridization by array (6)
Cell line - High-throughput sequencing (4)
DNA-seq (4)
Human - High-throughput sequencing (2)
High-throughput sequencing (2)
Bisulfite-seq (2)
ATAC-seq (2)
ScATAC-seq (2)
CUT&RUN (2)
Baseline (1)
MeDIP-seq (1)
Animal - One-color microarray (1)
Human - Single-cell sequencing (1)
Genotyping by array (1)
Capture-C (1)
CLIP-seq (1)

Release Date

2015 (303)
2014 (301)
2013 (289)
2012 (289)
2011 (257)
2016 (239)
2010 (238)
2009 (176)
2022 (161)
2021 (152)
2019 (146)
2008 (139)
2023 (138)
2018 (133)
2024 (128)
2020 (125)
2017 (122)
2025 (112)
2006 (71)
2007 (64)
2005 (53)
2004 (38)
2000 (28)
2026 (25)
1999 (23)
2001 (22)
2002 (21)
1998 (21)
2003 (16)
1997 (4)

Lab affiliation

1. College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China; 2. Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China (1)
Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany (1)
Hainan University (1)
Prof. Dr. Henning Urlaub Max-Planck-Institute for Biophysical Chemistry Bioanalytical Mass Spectrometry Group Am Fassberg 11 D-37077 Goettingen, Germany ************************************************ University Medical Center Goettingen Bioanalytics Institute for Clinical Chemistry Robert Koch Strasse 40 D-37075 Goettingen, Germany (1)
The University of Chicago Medicine Comprehensive Cancer Center, University of Chicago, Chicago, IL USA Department of Pathology Department of Pediatrics Committee on Cancer Biology (1)
Department of Biology, Stanford University (1)
Proteomics Center, Erasmus MC, Rotterdam (1)
Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA (1)
Biomedical & Life Sciences, Lancaster University UK (1)
Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel (1)
Molecular Pharmacology Program, Sloan Kettering Institute, Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, and Doctor of Medicine Program, Weill Cornell Medicine (1)
Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, 17104, South Korea. (1)
SPHERE research group, School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin (1)
Ramón y Cajal Fellow IBMCP (UPV/CSIC) Valencia, Spain (1)
Wallenberg Centre for Molecular Medicine (WCMM), Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden. (1)
Department of Biochemistry and Department of Bacteriology University of Wisconsin-Madison, Madison, WI 53706 Dept. of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 (1)
PPN Proteomics Plateform SFR Necker US24/CNRS UAR3633, Université Paris Cité, Paris, France (1)
Genetics & Experimental Bioinformatics University of Freiburg Institute of Biology III Schänzlestraße 1 D-79104 Freiburg Germany (1)
Ranish Lab, Institute for Systems Biology, USA (1)
Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Germany (1)
University of Wisconsin - Madison, Plant Pathology Department. (1)
School of Biosciences Firth Court, Western Bank University of Sheffield Sheffield, S10 2TN United Kingdom (1)
Department of Veterinary Sciences, Experimental Parasitology Ludwig-Maximilians-Universität München Leopoldstr. 5 80802 Munich Germany Biomedical Center Munich, Physiological Chemistry Ludwig-Maximilians-Universität München Großhaderner Str. 9 82152 Planegg-Martinsried Germany (1)
Department of Biochemistry 1, Theodor Boveri-Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany (1)
University of Pennsylvania (1)
Tsinghua university (1)
IMB, Ackermannweg 4, 55128 Mainz (1)
Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009,China (1)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (1)
Institute of Molecular Biology (1)

Tags

pathogen (37)
pathogen:bacterium (23)
pathogen:protozoan (9)
pathogen:virus (3)
pathogen:fungus (2)

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Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [TSS-Seq]

We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for two enterobacteria: Escherichia coli and Klebsiella pneumoniae.By obtaining over fourteen billion bases of sequence from 5' RACE (rapid amplification of cDNA ends) ...

ORGANISM(S): Escherichia coli K-12

2012-07-30 | E-GEOD-35821 | biostudies-arrayexpress

Genome-wide transcription start site determination of Geobacter sulfurreducens under multiple growth conditions

Determine the transcription start sites at 1-bp resolution across the entire G. sulfurreducens genome in multiple growth conditions, including fresh water acetate-fumarate (FWAF) medium, nitrogen limitation and growth on electrode. Special capture of the 5' end of primary transcripts in G. sulfurred...

ORGANISM(S): Geobacter sulfurreducens PCA

2010-07-01 | E-GEOD-22511 | biostudies-arrayexpress

Quality control of transcription start site selection by Nonsense-Mediated-mRNA Decay

Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficie...

ORGANISM(S): Saccharomyces cerevisiae BY4741

2015-04-24 | E-GEOD-64139 | biostudies-arrayexpress

Transcription start site identification in Bacillus subtilis

PRJEB35762 | ENA

Transcription Start Site (TSS) mapping and total RNAseq of Streptomyces scabies wild-type (WT) versus Streptomyces scabies ΔbtmL

The aim of this experiment was to map the transcription start sites (TSSs) in the bottromycin biosynthetic gene cluster from Streptomyces scabies, qualitatively assess the expression levels of this cluster within the bacterium's transcriptome and evaluate whether deletion of a potential regulatory g...

ORGANISM(S): Streptomyces scabiei

2020-02-19 | E-MTAB-8236 | biostudies-arrayexpress

5'RNA-seq analysis of hypertrophic cardiomyopathy (HCM) in mice that carry a human missence mutation in the myosin heavy chain

We developed a 5'RNA-seq methodology to concurrently assess gene expression and start-site usage changes. We applied this methodology to study hypertrophic cardiomyopathy in mice harboring a human deleterious mutation. 5'RNA-seq analysis of transcriptomes from mouse hearts with or without hypertroph...

ORGANISM(S): Mus musculus

2013-11-05 | E-GEOD-52038 | biostudies-arrayexpress

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

Transcription start site identification in Bacillus subtilis

Cappable-seq was used to map transcription start sites globally in wild type Bacillus subtilis. Total RNA was isolated from cells grown in LB media until exponential phase. RNA corresponding to transcription start sites was capped with a 5' biotin tag, which was used for enrichment via a pull down w...

ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168

2021-04-16 | E-MTAB-8582 | biostudies-arrayexpress

Ab initio identification of transcription start sites (TSSs) in the Rhesus macaque genome by histone modification and RNA-Seq

We addressed the lack of experimentally supported transcript annotations in the Rhesus macaque genome by ab initio identification of the transcription start sites (TSSs). We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)'s ability to mark TSSs and the recently developed ChIP-Seq and ...

ORGANISM(S): Macaca mulatta

2010-10-18 | E-GEOD-24538 | biostudies-arrayexpress

Transcription start site identification in wild type Escherichia coli

PRJEB40769 | ENA

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