Ice-chip - OmicsDI

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Transcriptomics (3402)
Genomics (1312)
Proteomics (58)
Unknown (14)
Metabolomics (5)

Organisms

Mus musculus (2074)
Homo sapiens (747)
Drosophila melanogaster (515)
Arabidopsis thaliana (262)
Caenorhabditis elegans (230)
Saccharomyces cerevisiae (111)
Rattus norvegicus (71)
Schizosaccharomyces pombe (44)
Candida albicans (39)
Rhizobium leguminosarum (26)
Danio rerio (24)
Escherichia coli (18)
Gallus gallus (16)
Streptomyces venezuelae (15)
Triticum aestivum (10)
Escherichia coli K-12 (9)
Salmonella enterica subsp. enterica serovar Typhimurium (8)
Zea mays (7)
Escherichia coli str. K-12 substr. MG1655 (7)
Streptomyces coelicolor A3(2) (6)
Vitis vinifera (6)
Bacillus subtilis (6)
Saccharomyces cerevisiae S288C (6)
Pseudomonas aeruginosa (6)
Lodderomyces elongisporus NRRL YB-4239 (5)
Folsomia candida (5)
Paxillus involutus (5)
Anopheles gambiae (5)
Mycobacterium tuberculosis (5)
Mycolicibacterium smegmatis MC2 155 (5)

Organisms

Mus musculus (41)
Homo sapiens (29)
Saccharomyces cerevisiae (16)
Rattus norvegicus (9)
Escherichia coli (5)
Pseudomonas aeruginosa (2)
Ceratina calcarata (2)
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Repository

biostudies-arrayexpress (4588)
ENA (123)
pride (45)
geo (14)
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Wood (1)
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Disease

Normal (23)
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Epithelioid mesothelioma (1)
Large cell carcinoma (1)
Invasive pituitary adenoma (1)
CUP (1)
Ependymoma (1)
Uninfected 11dpi (1)
Keratoconus (1)
Post-stasis (1)
Postnatal day 18 was the earliest time point at which structural differences between testes from wild-type and pcd3J-/- mice were observed via histopathology. (1)
Colorectal cancer recurrence-free (1)
Neuroblastoma-undifferentiated (1)

Technology Type

Mass Spectrometry (45)
Shotgun proteomics (25)
Gel-based experiment (12)
Affinity purification coupled with mass spectrometry proteomics (11)
Bottom-up proteomics (5)
Mass spectrometry (3)
Mass spectrometry assay (2)
Top-down proteomics (2)
Data-dependent acquisition (2)
MSE (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (152)
NextSeq 500 (79)
Illumina HiSeq 2000 (74)
Illumina HiSeq 2500 (60)
Illumina HiSeq 4000 (58)
BGISEQ-500 (54)
DNBSEQ-T7 (41)
NextSeq 550 (32)
NextSeq 2000 (15)
Illumina Genome Analyzer II (13)
Illumina Genome Analyzer IIx (12)
Illumina MiSeq (11)
Illumina HiSeq 3000 (10)
Ion Torrent Proton (8)
Illumina HiSeq 1500 (8)
GenePix 4000A [Axon Instruments] (5)
Axon GenePix 4000B scanning hardware (5)
Axon GenePix 4000A scanning hardware (4)
Axon- GenePix4000B (4)
Illumina NovaSeq X (4)
10x Genomics Chromium Controller (4)
Element AVITI (3)
Axon GenePix4000B (3)
Other (3)
G2565BA DNA microarray scanner [Agilent] (3)
GenePix 4000B [Axon Instruments] (3)
NextSeq 1000 (3)
NA (3)
Illumina HiSeq 1000 (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)

Publication Date

2013 (788)
2010 (488)
2014 (479)
2011 (470)
2015 (455)
2012 (420)
2016 (293)
2008 (167)
2009 (163)
2023 (104)
2007 (103)
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2024 (62)
2019 (56)
2006 (55)
2018 (50)
2017 (37)
2005 (34)
2004 (22)
2002 (1)
2003 (1)

Metabolite Name

2,3-DPG (1)
D-Ribulose-5-phosphate (1)
D-Glucose-1-phosphate (1)
Flavin-mononucleotide (1)
Isocitric-acid (1)
Dihydroxyacetone-phosphate (1)
6-Phosphogluconic-acid (1)
Phosphoenolpyruvic-acid (1)
C-di-AMP (1)
Fumaric-acid (1)
Citric-acid (1)
3-phenyllactic-acid (1)
Cysteic-acid (1)
Glucuronic-acid (1)
Triphosphate-guanosine (1)
2-Oxoadipic-acid (1)
D-Ribose-5-phosphate-disodium (1)
DL-Glyceric-Acid (1)
Glycolic-acid (1)
L-2-Hydroxyglutaric-acid-disodium (1)
Alpha-Ketoglutaric-Acid (1)
L-Glutamic-acid (1)
Pyruvic-acid (1)
Itaconic-acid (1)
NicotinaMide-adenine-dinucleotide(NAD) (1)
Cis-Aconitic-acid (1)
Malic-acid (1)
Xylulose-5-phosphate (1)
Dihydronicotinamide-adenine-dinucleotide-phosphate(NADPH) (1)
D(+)-Glucose (1)

First Public Date

2014 (41)
2024 (13)
2025 (12)
2023 (9)
2022 (9)
2021 (9)
2026 (8)
2020 (7)
2016 (4)
2019 (3)
2018 (3)
2015 (3)
2013 (2)

Classification

bacteria (10)

Modification

N6 (1)
N6-dimethyl-L-lysine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (1896)
ChIP-seq (1070)
ChIP-chip by tiling array (599)
RNA-seq of coding RNA (266)
RNA-seq of coding RNA from single cells (148)
ChIP-chip by array (113)
DNA-seq (80)
Methylation profiling by array (63)
Comparative genomic hybridization by array (53)
Unknown experiment type (33)
Other (31)
Methylation profiling by high throughput sequencing (28)
Transcription profiling by tiling array (25)
Cell line - High-throughput sequencing (22)
MicroRNA profiling by array (18)
Animal - High-throughput sequencing (15)
RNA-seq of non coding RNA (14)
ATAC-seq (12)
Single nucleus RNA sequencing (10)
High-throughput sequencing (9)
Animal - One-color microarray (7)
Animal - Single-cell sequencing (7)
Proteomic profiling by array (5)
RNA-seq of total RNA (5)
Genotyping by array (4)
CUT&RUN (4)
Cell line - Single-cell sequencing (3)
Transcription profiling by RT-PCR (3)
ScATAC-seq (3)
Baseline (2)

Release Date

2013 (788)
2010 (488)
2014 (479)
2011 (470)
2015 (455)
2012 (419)
2016 (292)
2008 (167)
2009 (162)
2007 (103)
2023 (95)
2021 (92)
2026 (81)
2022 (79)
2025 (71)
2020 (60)
2006 (56)
2024 (55)
2019 (52)
2018 (48)
2017 (37)
2005 (33)
2004 (19)
2002 (1)

Lab affiliation

Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany (2)
Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstraße 15, 04318 Leipzig, Germany (2)
Sunitha Nagrath Lab, 2800 Plymouth Rd, NCRC Building 10, Ann Arbor, MI- 48109 (1)
Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria (1)
Helmholtz-Centre for Environmental Research - UFZ Leipzig, Germany (1)
Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (1)
gurdon institute (1)
Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstra��e 15, 04318 Leipzig, Germany Phone +49 341 235 4767 nico.jehmlich@ufz.de, www.ufz.de (1)
Dr. Sanjeeva Srivastava, Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India (Lab head). (1)
Department of Molecular Genetics and Cell Biology and Ludwig Center for Metastasis Research, The University of Chicago, Chicago IL (1)
RNA-Protein Complexes & Cell Proliferation (B150) German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg, Germany (1)
Universitat Autònoma de Barcelona (1)
CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (1)
IBERS, Aberystwyth University (1)
Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 81377, Germany (1)
Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 58 Abrahama St., 80-307 Gdansk, Poland (1)
Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA (1)
Faculty of Health and Medical Sciences University of Surrey (1)
Helmholtz Pioneer Campus, Helmholtz Zentrum München, Munich, Germany and Medical Faculty, Technical University of Munich, Munich, Germany (1)
Department of Biological Engineering Department of Chemistry Massachusetts Institute of Technology Cambridge, MA 02139 (1)
Department of Biochemistry and Biophysics Smilow Center for Translational Research Perelman School of Medicine University of Pennsylvania 3400 Civic Center Blvd Philadelphia, PA 19104 (1)
Institute of Pharmacology and Structural Biology (IPBS), CNRS, Toulouse (1)
Duke University (1)
Assistant Professor, Dept. of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762 (1)
Group Leader, Department of Molecular Microbiology (1)
Centre for Integrative Bee Research (CIBER) Department of Entomology University of California Riverside, CA 92521 United States of America (1)
Genome Insistute of Singapore (GIS) (1)
Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstraße 15 04318 Leipzig, Germany (1)
Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. (1)
European Institute of Oncology (1)

Tags

pathogen (10)
pathogen:bacterium (10)

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A disposable microcapsule array chip fabricated by ice printing combined with isothermal amplification for Salmonella DNA detection.

Not available

S-EPMC9090901 | biostudies-literature

ChIP-seq of bovine cells (MDBK) to study butyrate-induced histone modification

Utilizing next-generation sequencing technology, combined with ChIP (Chromatin Immunoprecipitation) technology to analyze histone modification (acetylation) induced by butyrate and to map the epigenomic landscape of normal histone H3, H4 Cells were treated with 10 mM butyrate for 24 hr, The cells we...

ORGANISM(S): Bos taurus

2014-01-24 | E-GEOD-38973 | biostudies-arrayexpress

Expression profile of EV71-infection-responsive miRNAs

We attempted to identify potential miRNAs that can regulate viral replication by screening host miRNAs in EV71-infected RD cells. To compare the differential expression of miRNAs in EV71-infected cells at different time points, miRNA expression profiles were analyzed using Agilent Human MicroRNA Arr...

ORGANISM(S): Homo sapiens

2016-07-03 | E-GEOD-75455 | biostudies-arrayexpress

Genome-wide binding of transcription factor IRF3

Genome-wide binding of IRF3 was analysed in MM1.S cells using ChIP-seq high-throughput approach. MM1.S cells were fixed in 1% formaldehyde (Alfa Aesar) for 15min at room temperature. cells were lysed with hypotonic lysis buffer for 15minutes followed by nuclear lysis buffer for 15min on ice. ChIP fo...

ORGANISM(S): Homo sapiens

2021-02-28 | GSE163481 | GEO

Single cell RNAseq of 12-week old AKIMBA versus WT mouse retina

Single-cell RNA sequencing was performed on retinal tissue from 12-week-old wild-type and Akimba (Ins2AkitaxVEGF+/-) mice, which are known to replicate features of clinical diabetic retinopathy. The aim of this study was to provide deeper insight into the complex network of molecular and cellular ch...

ORGANISM(S): Mus musculus

2020-05-23 | E-MTAB-9061 | biostudies-arrayexpress

ICE-A: A chromatin interaction-based tool for improved annotation of distal cis-regulatory elements reveals novel regulatory functions of lineage-restricted transcription factors in lymphocytic development [ChIP-Seq]

PRJNA1175616 | ENA

Microfluidic Cold-Finger Device for the Investigation of Ice-Binding Proteins.

Not available

S-EPMC5034346 | biostudies-literature

Transcription profiling of mouse Clcn5 knockout in proximal tubules of the kidney

Dent disease has multiple defects attributed to proximal tubule malfunction including low molecular weight proteinuria, aminoaciduria, phosphaturia and glycosuria. In order to understand the changes in kidney function of the Clc5 transporter gene knockout mouse model of Dent disease, we examined gen...

ORGANISM(S): Mus musculus

2008-06-11 | E-GEOD-10162 | biostudies-arrayexpress

ChIP-sequencing of the H3K4me1/2 in crypts from mice intestinal epithelium with intestinal epithelium specific LSD1 knock out compared to wild type

To study the epigenetic regulation of intestinal epithelium we focus on the role of chromatin modulators. Lysine-specific histone demethylase 1a (KDM1A, LSD1) is one of the enzymes that can erase the H3K4me1/2 mark. To assess the role of LSD1 in intestinal epithelium we studied wild type (WT) (Villi...

ORGANISM(S): Mus musculus

2020-11-16 | E-MTAB-7871 | biostudies-arrayexpress

The Iron control element, acting in positive and negative control of iron-regulated Bradyrhizobium japonicum genes, is a target for the Irr protein.

Not available

S-EPMC1347296 | biostudies-literature

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