John S L SL - OmicsDI

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Transcriptomics (1050)
Unknown (554)
Genomics (133)
Proteomics (18)
Metabolomics (6)
Other (1)

Organisms

Homo sapiens (397)
Mus musculus (291)
Arabidopsis thaliana (75)
Rattus norvegicus (56)
Caenorhabditis elegans (33)
Streptomyces coelicolor (18)
Bos taurus (18)
Drosophila melanogaster (18)
Salmo salar (17)
Saccharomyces cerevisiae (15)
Methanococcus maripaludis S2 (12)
Daphnia pulex (12)
Glycine max (11)
Danio rerio (11)
Escherichia coli (9)
Streptomyces venezuelae (8)
Sus scrofa (7)
Picea glauca (5)
Solenopsis invicta (5)
Campylobacter jejuni (5)
Bacillus subtilis (5)
Staphylococcus aureus (5)
Cryptococcus neoformans (5)
Brassica rapa (4)
Rattus rattus (4)
Candida albicans (4)
Salmonella enterica (3)
Taeniopygia guttata (3)
synthetic construct (3)
Zea mays (3)

Repository

biostudies-arrayexpress (1141)
EGA (45)
MassIVE (9)
pride (7)
GNPS (3)
MetaboLights (3)
GPMDB (1)
jPOST (1)
PanoramaPublic (1)

Tissue

Cell culture (2)
T cell (2)
Blood plasma (1)
Melanocyte (1)
Permanent cell line cell (1)

Disease

Normal (6)
Severe acute respiratory syndrome (2)
Melanoma (2)
Benign nevi (1)
K173 influenza (1)
Infected with IBDV strain F52/70 (1)
Colorectal cancer recurrence-free (1)
Imatinib-resistant CML cell line subclone (1)
MFC II (1)
Dukes D primary colon cancer (1)
Systemic sclerosis with diffuse scleroderma (1)
Colon cancer metastasis (1)
Colorectal cancer (1)
Colon carcinoma (1)
None- acute control (1)
Small cell lung carcinoma (1)
Infant SGA (1)
Benign adenoma (1)
Cancer (1)
None- Acute Control (1)
S enteritidis (1)
Idiopathic dilated cardiomyopathy (1)
Acute promyelocytic leukemia (1)
Prostate cancer (1)
Multiple myeloma (1)
Invasive ductal carcinoma (1)
Acute myeloid leukemia (1)
Not Available (1)
Alveolar soft part sarcoma (1)
Bone cancer (1)

Technology Type

Illumina 15K (8)
Mass Spectrometry (7)
Bottom-up proteomics (3)
Shotgun proteomics (3)
Illumina HiSeq 2000 (2)
Illumina HiSeq 2500, ILLUMINA (2)
Mass spectrometry (2)
Illumina HiSeq 2000, Affymetrics_SNP_6.0-, Illumina Genome Analyzer IIx (1)
Illumina HiSeq 2000, Illumina Genome Analyzer IIx (1)
Illumina OncoArray (1)
Mass spectrometry assay (1)
NMR spectroscopy assay (1)
Affinity purification coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (33)
Illumina HiSeq 2500 (17)
Illumina HiSeq 2000 (16)
Illumina HiSeq 4000 (15)
NextSeq 500 (11)
NextSeq 2000 (4)
Illumina Genome Analyzer (2)
418 [Affymetrix] (2)
Illumina Genome Analyzer II (2)
Affymetrix Fluidics Station 400 (2)
Axon GenePix 4000B scanning hardware (2)
Illumina MiSeq (2)
NextSeq 550 (2)
Chromium Controller / Agilent Bioanalyzer (1)
Chromium Controller (1)
10X Genomics Chromium (1)
G2505. Agilent’s Scan Control software v. A.7.01 and Feature Extraction. (1)
C1 Single-Cell Auto Prep System, Fluidigm (1)
Axon Instruments GenePix 4000B scanner (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)
MoFlo XPD (Beckman Coulter, Fullerton, CA, USA) flow cytometer (1)
BD FACSARIA III (1)
Fluidigm C1 (1)
None (1)
Affymetrix Gene Titan (1)
Gene Titan (1)
Other (1)
GenePix Personal 4100A [Axon Instruments] (1)
Other (1)
Illumina Genome Analyzer IIx (1)

Publication Date

2011 (136)
2010 (129)
2012 (126)
2013 (125)
2014 (117)
2008 (101)
2015 (89)
2016 (71)
2009 (47)
2005 (45)
2007 (36)
2018 (21)
2006 (20)
2021 (16)
2022 (14)
2026 (13)
2023 (12)
2025 (10)
2020 (7)
2017 (7)
2003 (7)
2024 (6)
2019 (6)
2004 (2)
2002 (1)

CHEBI ID

CHEBI:15354 (2)
CHEBI:15428 (2)
CHEBI:15611 (2)
CHEBI:15698 (2)
CHEBI:15724 (2)
CHEBI:15741 (2)
CHEBI:15756 (2)
CHEBI:15891 (2)
CHEBI:16040 (2)
CHEBI:16235 (2)
CHEBI:16335 (2)
CHEBI:16344 (2)
CHEBI:16449 (2)
CHEBI:16450 (2)
CHEBI:16530 (2)
CHEBI:16610 (2)
CHEBI:16704 (2)
CHEBI:16708 (2)
CHEBI:16750 (2)
CHEBI:16765 (2)
CHEBI:16811 (2)
CHEBI:17012 (2)
CHEBI:17084 (2)
CHEBI:17126 (2)
CHEBI:17154 (2)
CHEBI:17172 (2)
CHEBI:17376 (2)
CHEBI:17533 (2)
CHEBI:17562 (2)
CHEBI:17568 (2)

Metabolite Name

N-acetylcitrulline (2)
P-cresol sulfate (2)
(7Z,10Z)-hexadecadienoylcarnitine (1)
(9Z,12Z)-3-hydroxyhexadecadienoylcarnitine (1)
1,11-Undecanedicarboxylic acid (1)
1,3-dimethylurate (1)
1-(1-enyl-palmitoyl)-2-arachidonoyl-GPC (P-16:0/20:4) (1)
1-(1-enyl-palmitoyl)-2-arachidonoyl-GPE (P-16:0/20:4) (1)
1-(1-enyl-palmitoyl)-2-linoleoyl-GPC (P-16:0/18:2) (1)
1-(1-enyl-palmitoyl)-2-linoleoyl-GPE (P-16:0/18:2) (1)
1-(1-enyl-palmitoyl)-2-palmitoyl-GPC (P-16:0/16:0) (1)
1-(1-enyl-palmitoyl)-GPE (P-16:0) (1)
1-(1-enyl-stearoyl)-2-linoleoyl-GPE (P-18:0/18:2) (1)
1-(1-enyl-stearoyl)-GPE (P-18:0) (1)
1-arachidonoyl-GPC (20:4n6) (1)
1-arachidonoyl-GPI (20:4) (1)
1-linoleoyl-2-arachidonoyl-GPC (18:2/20:4n6) (1)
1-linoleoyl-GPC (18:2) (1)
1-linoleoyl-GPE (18:2) (1)
1-methylguanidine (1)
1-methylhistidine (1)
1-methylnicotinamide (1)
1-methylxanthine (1)
1-oleoyl-2-linoleoyl-GPC (18:1/18:2) (1)
1-oleoyl-GPC (18:1) (1)
1-oleoyl-GPI (18:1) (1)
1-palmitoyl-2-arachidonoyl-GPC (16:0/20:4) (1)
1-palmitoyl-2-arachidonoyl-GPE (16:0/20:4) (1)
1-palmitoyl-2-arachidonoyl-GPI (16:0/20:4) (1)
1-palmitoyl-2-linoleoyl-GPC (16:0/18:2) (1)

Modification

2x(15)N labeled L-lysine (1)

Study type

Transcription profiling by array (725)
RNA-seq of coding RNA (141)
ChIP-seq (66)
Comparative genomic hybridization by array (26)
RNA-seq of coding RNA from single cells (25)
Methylation profiling by array (22)
RNA-seq of non coding RNA (22)
Transcription profiling by tiling array (20)
Methylation profiling by high throughput sequencing (17)
Unknown experiment type (11)
Other (8)
Genotyping by array (7)
ChIP-chip by tiling array (5)
Animal - High-throughput sequencing (5)
ChIP-chip by array (5)
MicroRNA profiling by array (5)
DNA-seq (5)
Transcription profiling by SAGE (3)
High-throughput sequencing (3)
Transcription profiling by RT-PCR (3)
Single nucleus RNA sequencing (3)
RNA-seq of total RNA (3)
ATAC-seq (2)
Baseline (1)
Differential (1)
Animal - One-color microarray (1)
Cell line - One-color microarray (1)
Cell line - High-throughput sequencing (1)
Genotyping by high throughput sequencing (1)

Release Date

2011 (156)
2012 (145)
2010 (142)
2013 (138)
2014 (136)
2015 (120)
2008 (106)
2016 (100)
2021 (80)
2022 (65)
2025 (58)
2009 (56)
2020 (53)
2024 (49)
2018 (46)
2005 (45)
2017 (41)
2023 (40)
2007 (39)
2019 (32)
2006 (22)
2026 (15)
2003 (7)
2004 (3)
2002 (1)

Lab affiliation

Roswell Park Cancer Center Buffalo, NY, USA (2)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (1)
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada (1)
Department of the Institute of Medical Sciences, Division of Nephrology (1)
Laboratory of Macromolecules and Interactomes,ERIBA-UMCG, Groningen, The Netherlands (1)
School of Life Sciences Faculty of Sciences University of Technology Sydney Australia (1)

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Transcription profiling of tomato - wax biosynthesis of PS mutant fruits

Mature green fruits of the tomato (Solanum lycopersicum L.) cultivar John Baer and Pearson were investigated (fruit developmental category II). John Baer wild type, John Baer LA0063 and Pearson wild type, Pearson 2-303 fruits were used. Tomato mutant plants LA0063 and 2-303 were positional sterile (...

ORGANISM(S): Lycopersicon esculentum

2009-06-09 | E-MEXP-2164 | biostudies-arrayexpress

Clonal Immortalized Human Glial Cell Lines Support Varying Levels of JC Virus Infection due to Differences in Cellular Gene Expression

JC virus (JCV) is a ubiquitous human polyomavirus that causes the demyelinating disease Progressive Multifocal Leukoencephalopathy (PML). JCV replicates in limited cell types in culture, predominantly in human glial cells. Thus, productive JCV infection is an indicator of the host cell transcription...

ORGANISM(S): Homo sapiens

2013-10-17 | E-GEOD-45639 | biostudies-arrayexpress

Transcription profiling of human bronchial epithelial cells stimulated with the commensal bacterium S. salivarius K12 of the pathogens S. aureus, P. aeruginosa, or S. enteritidis

Human bronchial epithelial cells (16HBE14O-) were stimulated with the commensal bacterium S. salivarius K12, or the pathogens S. aureus, P. aeruginosa, or S. enteritidis (subtype Typhimurium) for 1 hour.

ORGANISM(S): Homo sapiens

2008-10-30 | E-FPMI-13 | biostudies-arrayexpress

Differentiation of human fetal multipotential neural progenitor cells to astrocytes reveals susceptibility factors for JC Virus

Viral infections of the CNS are of increasing concern, especially among immunocompromised populations. Rodent models are often inappropriate for studies of CNS infection, as many viruses, including JC Virus (JCV) and HIV, cannot replicate in rodent cells. Consequently, human fetal brain-derived mult...

ORGANISM(S): Homo sapiens

2013-04-09 | E-GEOD-43794 | biostudies-arrayexpress

S. coelicolor M145 Time-course Study in R5- medium (Culture# 3)

Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this stud...