Binding site mapping

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Unknown (1224)
Genomics (932)
Transcriptomics (853)
Proteomics (131)
Other (28)
Metabolomics (3)
Genomic (1)
Methylation profiling (1)

Organisms

Homo sapiens (635)
Mus musculus (389)
Drosophila melanogaster (216)
Saccharomyces cerevisiae (72)
Arabidopsis thaliana (58)
Caenorhabditis elegans (43)
Rattus norvegicus (18)
Danio rerio (17)
Schizosaccharomyces pombe (13)
Zea mays (12)
Oryza sativa (12)
Escherichia coli str. K-12 substr. MG1655 (8)
Gallus gallus (7)
Escherichia coli (7)
Drosophila simulans (6)
Plasmodium falciparum (6)
Drosophila yakuba (5)
Bos taurus (5)
Sus scrofa (5)
Drosophila pseudoobscura (4)
synthetic construct (4)
Streptomyces venezuelae (4)
Streptomyces griseus (3)
Saccharomyces cerevisiae S288C (3)
Candida albicans (3)
Camponotus floridanus (2)
Euglena gracilis (2)
Equus caballus (2)
Chlamydomonas reinhardtii (2)
Streptomyces coelicolor A3(2) (2)

Organisms

Homo sapiens (62)
Mus musculus (21)
Saccharomyces cerevisiae (9)
Drosophila melanogaster (6)
Arabidopsis thaliana (5)
Oryza sativa (3)
Caenorhabditis elegans (2)
Nitratidesulfovibrio vulgaris (1)
Staphylococcus aureus subsp. aureus USA300 (1)
Sphingopyxis granuli (1)
Human immunodeficiency virus (1)
Escherichia coli str. K-12 substr. MG1655 (1)
Leptospira interrogans serovar Manilae (1)
Caulobacter vibrioides NA1000 (1)
Durio zibethinus (1)
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (1)
Human immunodeficiency virus 1 (1)
Pseudomonas aeruginosa PAO1 (1)
Serratia marcescens (1)
Escherichia coli K-12 (1)
Bacillus subtilis (1)
Pseudomonas aeruginosa (1)
Staphylococcus aureus (1)
Plasmodium falciparum (1)
Toxoplasma gondii (1)
synthetic construct (1)

Repository

biostudies-arrayexpress (1541)
ENA (152)
geo (121)
pride (91)
MassIVE (22)
PeptideAtlas (6)
EGA (4)
iProX (4)
MetaboLights (2)
dbGaP (1)
GNPS (1)
GPMDB (1)
jPOST (1)
PanoramaPublic (1)
PAXDB (1)

Tissue

Cell culture (30)
Epithelial cell (11)
Others (6)
B cell (5)
T cell (5)
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Leaf (3)
Liver (3)
Permanent cell line cell (3)
Plant cell (3)
Blood (2)
Root (2)
Blood cell (1)
Blood serum (1)
Brain (1)
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Cell suspension culture (1)
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Lung (1)
Macrophage (1)
Melanocyte (1)
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Peripheral blood mononuclear cell (1)
Prostate epithelium cell (1)

Disease

Normal (3)
Cervix carcinoma (3)
Lymphoma (3)
Breast cancer (2)
Breast carcinoma (1)
Not Available (1)
Acrodysostosis (1)
Acute leukemia (1)
Alzheimer's disease (1)
Avian influenza (1)
Babesiosis (1)
Breast ductal carcinoma (1)
Cardiovascular system disease (1)
Colon cancer (1)
Disease free (1)
Inflammation (1)
Leishmaniasis (1)
Liver disease (1)
Melanoma (1)

Technology Type

Mass Spectrometry (91)
Shotgun proteomics (53)
Affinity purification coupled with mass spectrometry proteomics (20)
Bottom-up proteomics (16)
Data-dependent acquisition (6)
Chemical cross-linking coupled with mass spectrometry proteomics (4)
SWATH MS (4)
Mass spectrometry (2)
Data-independent acquisition (2)
Mass spectrometry imaging (2)
Top-down proteomics (2)
Affinity proteomics (1)
All-ion fragmentation (1)
DiaPASEF (1)
Gel-based experiment (1)
MSE (1)
SRM/MRM (1)

Instrument Platform

Illumina HiSeq 2000 (38)
Illumina NovaSeq 6000 (32)
Illumina HiSeq 2500 (31)
NextSeq 500 (26)
Illumina HiSeq 4000 (19)
Illumina MiSeq (8)
NextSeq 550 (8)
Illumina Genome Analyzer II (5)
Illumina Genome Analyzer IIx (4)
Illumina NovaSeq X (3)
10x Genomics Chromium Controller (3)
Ion Torrent Proton (3)
NextSeq 2000 (2)
Illumina HiSeq 1500 (2)
FastPrep-24 5G bead beater, Qubit Fluorometer (1)
12 well TC-treated plate, LETs buffer, dry ice (1)
Nikon Eclipse Ti2 with brightfield and fluorescence capacity (TRITC) (1)
Leica Biosystems Cryostat (1)
Qubit 4.0 and TapeStation (1)
Element AVITI (1)
Bio-Rad CFX96 Real-time System (1)
Illumina Genome Analyser II (1)
MA900, Sony (1)
10x Chromium Controller (1)
FACS (1)
Illumina HiSeq2500 (1)
Dell PowerEdge 630 with Intel Xeon E5-2630 processor (8 cores 16 threads) and 94 GB memory running CentOS Linux release 7.5.1804. (1)
FACSAria (BD) (1)
Not applicable (1)
454 GS 20 (1)

Publication Date

2013 (306)
2014 (221)
2015 (192)
2012 (183)
2011 (168)
2010 (165)
2016 (97)
2009 (53)
2021 (49)
2026 (42)
2008 (39)
2020 (37)
2019 (37)
2024 (33)
2022 (33)
2025 (30)
2018 (28)
2023 (27)
2017 (18)
2007 (14)
2006 (7)
2005 (3)
2004 (1)

UNIPROT ID/AC

35KD_MYCTU (1)
3BHS_MYCTU (1)
3MGH_MYCTU (1)
83332.Rv1180 (1)
83332.Rv1370c (1)
83332.Rv1757c (1)
83332.Rv1763 (1)
83332.Rv2098c (1)
83332.Rv2105 (1)
83332.Rv2168c (1)
83332.Rv2278 (1)
83332.Rv2354 (1)
83332.Rv2480c (1)
83332.Rv2648 (1)
83332.Rv2815c (1)
83332.Rv3117 (1)
83332.Rv3118 (1)
83332.Rv3184 (1)
83332.Rv3186 (1)
83332.Rv3325 (1)
83332.Rv3381c (1)
83332.Rv3474 (1)
83332.Rv3514 (1)
83332.Rv3619c (1)
A85A_MYCTU (1)
A85B_MYCTU (1)
A85C_MYCTU (1)
AAC2_MYCTU (1)
ABC1_MYCTU (1)
ACDP_MYCTU (1)

ENSEMBL ID

ENSG00000170477 (5)
ENSG00000247315 (4)
ENSG00000147251 (1)

CHEBI ID

CHEBI:27524 (1)
CHEBI:186165 (1)
CHEBI:167190 (1)
CHEBI:167189 (1)
CHEBI:167188 (1)
CHEBI:167187 (1)
CHEBI:167186 (1)
CHEBI:167185 (1)
CHEBI:16996 (1)
CHEBI:183136 (1)
CHEBI:88493 (1)
CHEBI:1958 (1)
CHEBI:17282 (1)
CHEBI:170068 (1)
CHEBI:170157 (1)
CHEBI:170156 (1)
CHEBI:186499 (1)
CHEBI:53013 (1)
CHEBI:165564 (1)
CHEBI:170122 (1)
CHEBI:86072 (1)
CHEBI:16485 (1)
CHEBI:63979 (1)
CHEBI:73028 (1)
CHEBI:156190 (1)
CHEBI:27584 (1)
CHEBI:72733 (1)
CHEBI:53488 (1)
CHEBI:28125 (1)
CHEBI:86543 (1)

Metabolite Name

9,10,18-trihydroxyoctadecanoic acid (1)
Ceramide phosphoethanolamine (d31:0) (1)
Ceramide phosphoethanolamine (t35:0) (1)
1-octadecyl-sn-glycero-3-phosphoinositol-3-phosphate (1)
Phosphatidylinositol (12:0) (1)
18-hydroxycorticosterone (1)
Thiamine(1+) diphosphate (1)
2,2',2''-((2R,5R,8S,11R)-11-((2R,4S,5E,7E,9E)-2,4-dihydroxypentadeca-5,7,9-trien-1-yl)-3,6,9,13,17-pentaoxo-1,4,7,10,14-pentaazacycloheptadecane-2,5,8-triyl)triacetamide (1)
(3R,5R,7S,8E,10E,12E)-3-amino-5,7-dihydroxyoctadeca-8,10,12-trienoic acid (1)
(3-((3R,5R,7S,8E,10E,12E)-3-amino-5-hydroxy-7-methoxyoctadeca-8,10,12-trienamido)propanoyl)-D-asparaginyl-D-asparagine (1)
(3-((3R,5R,7S,8E,10E,12E)-3-amino-5-hydroxy-7-methoxyoctadeca-8,10,12-trienamido)propanoyl)-D-asparagine (1)
3-((3R,5R,7S,8E,10E,12E)-3-amino-5-hydroxy-7-methoxyoctadeca-8,10,12-trienamido)propanoic acid (1)
(3R,5R,7S,8E,10E,12E)-3-amino-5-hydroxy-7-methoxyoctadeca-8,10,12-trienoic acid (1)
11-dehydrocorticosterone (1)
2-hydroxyoctanoic acid (1)
PA(20:2(11Z,14Z)/15:0) (1)
PA(15:0/20:2(11Z,14Z)) (1)
9,10,13-Trihydroxystearic acid (1)
Ubiquinone-1 (1)
Aldosterone (1)

First Public Date

2014 (18)
2026 (16)
2013 (15)
2018 (13)
2021 (12)
2022 (10)
2020 (10)
2025 (9)
2024 (9)
2017 (9)
2016 (9)
2019 (8)
2023 (7)
2015 (6)
2010 (1)

Classification

bacteria (9)
viruses (2)
protozoa (2)

Study type

ChIP-seq (654)
RNA-seq of coding RNA (312)
Transcription profiling by array (164)
Other (77)
Methylation profiling by high throughput sequencing (60)
ChIP-chip by tiling array (53)
Comparative genomic hybridization by array (36)
RNA-seq of non coding RNA (27)
Methylation profiling by array (21)
Unknown experiment type (17)
RNA-seq of coding RNA from single cells (17)
ChIP-chip by array (13)
DNA-seq (9)
Cell line - High-throughput sequencing (8)
Transcription profiling by tiling array (8)
CLIP-seq (7)
ATAC-seq (7)
High-throughput sequencing (5)
Hi-C (5)
Animal - High-throughput sequencing (4)
Proteomic profiling by array (4)
CLIP-Seq (3)
Human - High-throughput sequencing (3)
Genotyping by array (3)
Ribo-seq (3)
CUT&RUN (3)
RNA-seq of total RNA (3)
Transcription profiling by SAGE (2)
RIP-seq (2)
Transcription profiling by high throughput sequencing (1)

Release Date

2013 (358)
2014 (279)
2015 (254)
2012 (232)
2011 (225)
2010 (204)
2016 (166)
2021 (90)
2020 (90)
2025 (87)
2009 (85)
2022 (84)
2008 (83)
2019 (77)
2018 (77)
2023 (73)
2024 (60)
2017 (60)
2007 (41)
2026 (30)
2006 (28)
2005 (18)
2004 (13)
2002 (11)
2000 (10)
2001 (9)
2003 (6)
1999 (6)
1998 (5)
1997 (3)

Lab affiliation

Department of Chemistry and Chemical Biology, Harvard University (3)
University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR (3)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (2)
college of pharmacy, Nankai university,Tianjin, 300353, China (2)
1 VIB-UGent Center for Medical Biotechnology, B9052 Ghent, Belgium; 2 Department of Biomolecular Medicine, Ghent University, B9052 Ghent, Belgium. (1)
1. Center for Medical Biotechnology, VIB, Ghent, Belgium 2. Department for Biomolecular Medicine, Ghent University, Ghent, Belgium 3. VIB Proteomics Core, VIB, Ghent, Belgium (1)
1. Center for Medical Biotechnology, VIB, Ghent, Belgium. 2. Department for Biomolecular Medicine, Ghent University, Ghent, Belgium 3. VIB Proteomics Core, VIB, Ghent, Belgium (1)
1Department of Chemistry, Georgia State University, Atlanta, GA (1)
733 N. Broadway Miller Research Building room 527 Johns Hopkins University Baltimore, MD 21205 (1)
Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy (1)
Associate Professor Faculty of Biology Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel (1)
Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2052, Australia (1)
Chemical Proteomics, Division of Chemistry I, Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm, Sweden (1)
Clinical Proteomics Mass Spectrometry, Science for Life Laboratory, Dept. of Oncology Pathology, Karolinska Institutet (1)
Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA. (1)
Dana-Farber Cancer Institute Harvard Medical School (1)
Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary (1)
Department of Biochemistry, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada (1)
Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria (1)
Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland Faculty of Science, University of Zürich, Zürich, Switzerland (1)
Department of Cellular and Molecular Pharmacology, University of California, San Francisco (1)
Department of Chemical Physiology and Biochemistry Oregon Health & Science University 3181 SW Sam Jackson Park Road Portland, Oregon 97239, USA (1)
Department of Chemistry and Chemical Biology (1)
Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA, 02138 (1)
Department of Chemistry and Chemical Biology, Woo Lab, Harvard University, US (1)
Department of Chemistry, Imperial College London, United Kingdom (1)
Department of Chemistry, Scripps Research (1)
Department of Chemistry, Stanford University (1)
Department of Medicine (1)
Department of Molecular Medicine Department of Chemistry The Scripps Research Institute (1)

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MicroMap photoproximity labeling enables small molecule binding site mapping

Proteomics data for MicroMap enabled binding site mapping

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2023-05-26 | MSV000092043 | MassIVE

Saccharomyces cerevisiae 3' poly(A) site mapping

The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented ef...

ORGANISM(S): Saccharomyces cerevisiae

2013-01-10 | E-GEOD-40110 | biostudies-arrayexpress

BATSeq of ESC-FCS/ESC-2i/NSC

Single-cell polyadenylation site quantification 48 single cells each of murine embryonic stem cells maintained in FCS+LIF medium ("ESC"), embryonic stem cells maintained in serum free, 2i containing medium ("2i") and neural stem cells ("NSC") were sequenced by BATSeq, a...

ORGANISM(S): Mus musculus

2015-06-09 | E-GEOD-60768 | biostudies-arrayexpress

Mapping the biosynthetic pathway of a hybrid polyketide-nonribosomal peptide in a metazoan

Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) hybrid systems typically use complex protein-protein interactions to facilitate direct transfer of intermediates between these multimodular megaenzymes. In the canal-associated neurons (CANs) of Caenorhabditis elegans, PKS-1 and NR...

2021-06-22 | MTBLS2313 | MetaboLights

Genome-wide Binding Site Mapping of Estrogen Receptor alpha and c-MYC in Breast Cancer Cells

Estrogens are steroid hormones that play critical roles in the initiation, development, and metastasis of breast and uterine cancers. The estrogen (E2) response in breast cancer cells is predominantly mediated by the estrogen receptor-alpha (ER alpha), a ligand-activated transcription factor. ER a...

ORGANISM(S): Homo sapiens

2010-05-26 | E-GEOD-10800 | biostudies-arrayexpress

RRHP : a tag-based approach for 5-hydroxymethylcytosine mapping at single-site resolution

We present here a novel approach called Reduced Representation 5-Hydroxymethylcytosine Profiling (RRHP), which exploits ?-glucosyltransferase (?-GT) to inhibit restriction digestion at adapters ligated to a genomic library, such that only fragments presenting glucosylated 5hmC residues at adapter ju...

ORGANISM(S): Homo sapiens

2014-08-26 | E-GEOD-49546 | biostudies-arrayexpress

Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin

This SuperSeries is composed of the following subset Series: GSE32348: Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin (mRNA) GSE32349: Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin (ChIP-Seq) Refer to indivi...

ORGANISM(S): Homo sapiens

2011-10-06 | E-GEOD-32350 | biostudies-arrayexpress

Genomic mapping of cAMP receptor protein binding in relation to transcriptional start sites in Mycobacterium tuberculosis

In this study we have used ChIPseq analysis to perform comprehensive mapping of the binding profile of the cAMP receptor protein (CRPMt) of M. tuberculosis combined with RNAseq studies to further investigate the transcriptional response following crp gene deletion and under alternative growth condi...

ORGANISM(S): Mycobacterium tuberculosis

2014-06-24 | E-MTAB-2390 | biostudies-arrayexpress

Genome-wide mapping of Jun binding site (K562)

Proto-oncogene c-jun is a leucine-zipper containing transcription factor which has a DNA binding domain and a transactivation domain. Jun dimerizes with another transcription factor Fos to form AP1 transcription factor. The AP-1 complex has been implicated in transformation and progression of cancer...

ORGANISM(S): Homo sapiens

2009-12-31 | E-GEOD-19545 | biostudies-arrayexpress

Genome-wide mapping of Fos binding site (K562)

Proto-oncogene c-Fos is a leucine-zipper containing transcription factor which has a DNA binding domain and a transactivation domain. Fos dimerizes with another transcription factor Jun to form AP1 transcription factor. The AP-1 complex has been implicated in transformation and progression of cancer...

ORGANISM(S): Homo sapiens

2009-12-31 | E-GEOD-19546 | biostudies-arrayexpress

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3173 Results

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