Liang Chi C - OmicsDI

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Transcriptomics (2134)
Genomics (570)
Unknown (195)
Proteomics (10)
Metabolomics (7)

Organisms

Homo sapiens (1005)
Mus musculus (804)
Drosophila melanogaster (118)
Arabidopsis thaliana (111)
Saccharomyces cerevisiae (89)
Rattus norvegicus (65)
Caenorhabditis elegans (40)
Danio rerio (34)
Rhizobium leguminosarum (26)
Schizosaccharomyces pombe (26)
Escherichia coli (15)
Gallus gallus (13)
Escherichia coli str. K-12 substr. MG1655 (13)
Bos taurus (12)
Sus scrofa (11)
Sinorhizobium meliloti (10)
Salmonella enterica subsp. enterica serovar Typhimurium (9)
Candida albicans (9)
Zea mays (8)
Mytilus galloprovincialis (7)
Glycine max (7)
Escherichia coli K-12 (7)
Triticum aestivum (7)
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Bacillus subtilis (6)
Hordeum vulgare (6)
Saccharomyces cerevisiae SK1 (5)
Burkholderia multivorans (5)
Corynebacterium glutamicum (5)
Pseudomonas putida (5)

Repository

biostudies-arrayexpress (2703)
EGA (12)
MetaboLights (7)
pride (5)
iProX (4)

Tissue

Cell culture (4)
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Renal cortical epithelial cell (1)
Embryonic stem cell (1)

Disease

Normal (15)
Melanoma (3)
Infiltrating ductal carcinoma (2)
Breast adenocarcinoma (2)
Rheumatoid arthritis (2)
Chronic myeloid leukemia (2)
Osteosarcoma (2)
Prostate cancer (2)
Tumor bearing (1)
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Dermal neurofibroma (1)
Hepatomegaly (1)
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Post-stasis (1)
B. dendrobatidis infection (1)
Severe acute respiratory syndrome (1)
Plasmodium berghei-infected cells (1)
Infected (1)
Infected with Drechmeria coniospora (1)
Healthy (1)
Dukes D primary colon cancer (1)
Lung large cell carcinoma (1)
Colon cancer metastasis (1)
Infected (1)
Colon carcinoma (1)
Colorectal carcinoma (1)
IBDV infected (1)
Colon cancer (1)
Bladder transitional carcinoma (1)

Technology Type

Mass spectrometry (5)
Mass Spectrometry (5)
Affinity purification coupled with mass spectrometry proteomics (3)
Mass spectrometry assay (2)
Illumina_450K, Illumina_HumanHT-12_V4, ILLUMINA, Illumina HiSeq 2000 (1)
SRM/MRM (1)
Data-dependent acquisition (1)
Bottom-up proteomics (1)
Shotgun proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (130)
Illumina HiSeq 2000 (46)
Illumina HiSeq 4000 (45)
NextSeq 500 (44)
Illumina HiSeq 2500 (38)
NextSeq 2000 (14)
NextSeq 550 (14)
Illumina NovaSeq X (9)
Illumina Genome Analyzer IIx (8)
Illumina MiSeq (7)
AB SOLiD 4 System (5)
Axon GenePix 4000B scanning hardware (5)
NextSeq 1000 (5)
Other (4)
NA (4)
Illumina HiSeq 1500 (4)
GeneChip Scanner 3000 [Affymetrix] (3)
GenePix 4000B [Axon Instruments] (3)
Ion Torrent Proton (3)
N/A (3)
Illumina HiSeq 3000 (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)
Chromium Controller (2)
Bio-Rad CFX96 Real-time System (2)
BD LSRFortessa (2)
10X Genomics Chromium (2)
RiboZero (2)
None (2)
Trizol (Invitrogen); FastPrep (MP Biochemicals) (2)
DASGIP bioreactors (2)

Publication Date

2013 (347)
2012 (308)
2014 (304)
2010 (300)
2011 (288)
2015 (241)
2016 (158)
2008 (126)
2009 (119)
2007 (67)
2025 (66)
2026 (56)
2021 (50)
2022 (44)
2020 (38)
2018 (36)
2006 (33)
2024 (32)
2023 (27)
2005 (24)
2017 (23)
2019 (19)
2004 (12)

CHEBI ID

CHEBI:30769 (4)
CHEBI:30831 (3)
CHEBI:17626 (3)
CHEBI:35619 (3)
CHEBI:30816 (3)
CHEBI:17634 (3)
CHEBI:17230 (3)
CHEBI:16856 (3)
CHEBI:17126 (3)
CHEBI:16708 (3)
CHEBI:17562 (3)
CHEBI:16750 (3)
CHEBI:17748 (3)
CHEBI:16988 (3)
CHEBI:15428 (3)
CHEBI:15741 (3)
CHEBI:6650 (3)
CHEBI:16865 (3)
CHEBI:17196 (3)
CHEBI:30763 (3)
CHEBI:16335 (3)
CHEBI:15355 (3)
CHEBI:17509 (3)
CHEBI:18183 (3)
CHEBI:15843 (3)
CHEBI:15971 (3)
CHEBI:29016 (3)
CHEBI:16704 (3)
CHEBI:17053 (3)
CHEBI:16015 (3)

Metabolite Name

Thiamine (3)
Marmesin (2)
Tetracosanoic acid (2)
GTP (2)
Kanosamine (2)
Coniferin (2)
DCDP (2)
DTTP (2)
Galactitol (2)
L-Cystine (2)
L-Norleucine (2)
Vanillic acid (2)
Pentadecanoic acid (2)
Glycine (2)
UTP (2)
IMP (2)
CTP (2)
CDP-choline (2)
ATP (2)
L-Alanine (2)
Phenylacetic acid (2)
Kaempferol (2)
L-Lysine (2)
Eriodictyol (2)
3-Indoleacetonitrile (2)
Glutathione (2)
Syringic acid (2)
L-Proline (2)
CDP-ethanolamine (2)
Erucic acid (2)

Study type

Transcription profiling by array (1241)
ChIP-seq (536)
ChIP-chip by tiling array (196)
RNA-seq of coding RNA from single cells (166)
RNA-seq of coding RNA (147)
ChIP-chip by array (89)
Comparative genomic hybridization by array (81)
Methylation profiling by array (46)
Other (30)
Genotyping by array (23)
Unknown experiment type (18)
Methylation profiling by high throughput sequencing (15)
RNA-seq of non coding RNA (13)
Transcription profiling by tiling array (11)
Cell line - High-throughput sequencing (8)
MicroRNA profiling by array (8)
RNAi profiling by array (7)
DNA-seq (7)
Animal - Single-cell sequencing (6)
High-throughput sequencing (6)
Single nucleus RNA sequencing (6)
Differential (4)
Animal - High-throughput sequencing (4)
Human - High-throughput sequencing (3)
Baseline (2)
Human - Single-cell sequencing (2)
ATAC-seq (2)
ScATAC-seq (2)
RNA-seq of total RNA (2)
ChIP-chip by SNP array (1)

Release Date

2013 (351)
2014 (309)
2012 (309)
2010 (301)
2011 (292)
2015 (248)
2016 (169)
2008 (126)
2009 (119)
2025 (106)
2021 (72)
2007 (67)
2023 (61)
2022 (59)
2026 (54)
2024 (53)
2020 (43)
2018 (37)
2006 (33)
2017 (27)
2019 (26)
2005 (24)
2004 (12)

Lab affiliation

Chair, Department of Physiology University of Arizona College of Medicine - Tucson 1656 E Mabel St Tucson, AZ 85721 (1)
Emory Univerity (1)
Sun Yat-Sen University (1)
2The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China (1)
Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, China. (1)

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CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

Capture Hi-C (CHi-C) is a state-of-the art method for profiling chromosomal interactions involving targeted regions of interest (such as gene promoters) globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other ...

ORGANISM(S): Mus musculus

2016-05-18 | E-GEOD-81503 | biostudies-arrayexpress

Genome-wide analysis of germ cell proliferation in C. elegans

Proliferating germ cells in C. elegans provide a useful model system for deciphering fundamental mechanisms underlying the balance between proliferation and differentiation. Using gene expression profiling of mutants with excess germ cell proliferation, we identified approximately 200 genes express...

ORGANISM(S): Caenorhabditis elegans

2010-04-29 | E-GEOD-21531 | biostudies-arrayexpress

CRC CHi-C DAC

Data Access Committee EGAC00001000639

EGAC00001000639 | EGA

Differentially regulated genes in control and c-myc N-myc deficient LT-HSCs

Analysis of HSCs from control and c-myc N-myc deficient long-term hematopoietic stem cells. HSCs lacking both c-myc and N-myc display increased apoptosis rates. Data provide insight into the molecular changes occuring upon complete loss of Myc activity, clarifying the resulting apoptotic mechanism a...

ORGANISM(S): Mus musculus

2009-02-20 | E-GEOD-12467 | biostudies-arrayexpress

5' Cap-Isolated RNA Pol II Transcripts and ENCODE Tiling Arrays to Identify Gene Expression Changes in Hepatitis C Liver

Recent studies of the human transcriptome suggest that many transcripts have short or lack 3' poly(A) ends. In addition, the length of 3' poly(A) ends may vary for some transcript to regulate mRNA translation. Heterogeneous lengths of poly(A) ends may introduce variations in measuring RNA transcript...

ORGANISM(S): Homo sapiens

2011-03-29 | E-GEOD-18904 | biostudies-arrayexpress

Defining the Roles and Regulation of the GATA-factor ELT-2 in the C. elegans Endoderm

We identified genome-wide sites of occupancy for the intestine-specific transcription factor ELT-2 in L3-staged N2 worm by performing ELT-2 ChIP-seq on whole worms; we performed RNA-seq on L3-staged N2 whole worms To identify DNA regions of direct ELT-2 occupancy, we performed the following ChIP-seq...

ORGANISM(S): Caenorhabditis elegans

2016-03-30 | E-GEOD-71720 | biostudies-arrayexpress

Ethics of Controlled Human Infection Studies With Hepatitis C Virus.

Not available

S-EPMC10425137 | biostudies-literature

DNA binding activities of the C-clamp

Investigated the DNA binding specificity of the C-clamp of dnTCF1E Used a doxycycline inducible system to investigate the role of the C-clamp in the genome-wide binding of dnTCF1E. Induced dnTCF1EWT and dnTCF1Emut (C-clamp mutant that is null for C-clamp DNA binding) over 2 time points (2 hours and...

ORGANISM(S): Homo sapiens

2014-12-04 | E-GEOD-53536 | biostudies-arrayexpress

Smooth Muscle Cells

This set contains 68 arrays of two series of experiments. 60 arrays are used to profile the heterogeneity of SMCs from different anatomic locations. 8 arrays are used to profile the change of gene expression of vascular smooth muscle cells upon serum exposure. An all pairs experiment design type is ...

ORGANISM(S): Homo sapiens

2007-09-27 | E-GEOD-7195 | biostudies-arrayexpress

Tai Chi for improving balance and reducing falls: A protocol of systematic review and meta-analysis.

Not available

S-EPMC6831220 | biostudies-literature

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