Liang C L CL - OmicsDI

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Transcriptomics (1238)
Unknown (242)
Genomics (129)
Proteomics (15)
Metabolomics (5)

Organisms

Homo sapiens (483)
Mus musculus (373)
Arabidopsis thaliana (99)
Saccharomyces cerevisiae (52)
Drosophila melanogaster (48)
Rattus norvegicus (32)
Rhizobium leguminosarum (30)
Danio rerio (24)
Caenorhabditis elegans (16)
Daphnia magna (9)
Streptococcus pneumoniae D39 (8)
Trypanosoma brucei (7)
Triticum aestivum (7)
Escherichia coli (7)
Bos taurus (6)
Candida albicans (6)
Macaca mulatta (5)
Xenopus laevis (5)
Schizosaccharomyces pombe (5)
Gallus gallus (5)
Saccharomyces cerevisiae SK1 (4)
Streptomyces coelicolor (4)
Bacillus subtilis (4)
Escherichia coli K-12 (4)
Callithrix jacchus (3)
Felis catus (3)
Porphyromonas gingivalis (3)
Escherichia coli str. K-12 substr. MG1655 (3)
Azoarcus sp. (2)
Nicotiana attenuata (2)

Repository

biostudies-arrayexpress (1363)
EGA (9)
pride (9)
MetaboLights (5)
jPOST (3)
iProX (1)
PanoramaPublic (1)

Tissue

Cell culture (4)
Epithelial cell (1)
Fibroblast (1)
Hepatocyte (1)
Leaf (1)
Malignant cell (1)
Ovary cancer cell (1)

Disease

Normal (7)
Porphyria NOS (2)
Adenocarcinoma (2)
Ovarian tumor (2)
High risk B-precurser acute lymphoblastic leukemia (1)
Hepatitis C virus-induced hepatocellular carcinoma (1)
Hepatomegaly (1)
Wilms' tumor (1)
Pre-tumoral lesion in a mouse model of human adamantinomatous craniopharyngioma (ACP) (1)
Xenografts with H1299 cell line (1)
Hepatoblastoma (1)
Heterodera schachtii nematode infection (1)
"hepatocellular adenoma" (1)
Teratozoospermia and infertility (1)
Infected with Drechmeria coniospora (1)
ARR1-SRDX (1)
Colon carcinoma (1)
WT (1)
Melanoma (1)
Not infected (1)
These mice have a relatively normal first wave of spermatogenesis but never become fertile. Older animals show increased apoptosis of germ cells, increasing in severity as germ cell stage advances. (1)
Colorectal adenocarcinoma (1)
Breast carcinoma (1)
Neurofibromatosis type 1 (1)
Disease free (1)
Osteosarcoma (1)

Technology Type

Mass Spectrometry (9)
Shotgun proteomics (6)
Mass spectrometry (5)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
Affinity purification coupled with mass spectrometry proteomics (1)
Bottom-up proteomics (1)
Data-dependent acquisition (1)

Instrument Platform

NextSeq 500 (43)
Illumina NovaSeq 6000 (34)
NextSeq 550 (25)
Illumina HiSeq 2500 (19)
Illumina HiSeq 4000 (18)
Illumina MiSeq (13)
Illumina HiSeq 2000 (13)
Chromium 10x (7)
Illumina NovaSeq X (6)
NextSeq 2000 (6)
Axon- GenePix4000B (5)
Illumina Genome Analyzer II (4)
Scanning hardware (4)
AB SOLiD 4 System (3)
GenePix 4000A [Axon Instruments] (3)
Axon GenePix 4000B scanning hardware (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)
10x Chromium (2)
ScanArray 4000 [PerkinElmer] (2)
Illumina Genome Analyzer (2)
Generation III Scanner (2)
ScanArray 4000XL [PerkinElmer] (2)
Illumina HiSeq 3000 (2)
SnakePipes 3.4 (1)
NEBNext Ultra II DNA Library Prep Kit (1)
Chromium Controller with Chromium Next GEM Single Cell 5’ and V(D)J (kits v1.1) (1)
NextSeq 500, 75 bp single end lane (1)
KAPA EvoPrep Kit (1)
Chromium Next GEM Chip G (1)
10X v3 (1)

Publication Date

2013 (166)
2010 (146)
2015 (129)
2012 (121)
2014 (120)
2008 (108)
2011 (84)
2016 (78)
2009 (71)
2022 (56)
2007 (38)
2005 (36)
2021 (33)
2006 (31)
2026 (29)
2020 (22)
2025 (18)
2023 (18)
2024 (17)
2017 (17)
2018 (16)
2004 (11)
2019 (10)
2003 (6)

CHEBI ID

CHEBI:17154 (3)
CHEBI:138367 (2)
CHEBI:15354 (2)
CHEBI:15724 (2)
CHEBI:15756 (2)
CHEBI:16040 (2)
CHEBI:16335 (2)
CHEBI:16704 (2)
CHEBI:16708 (2)
CHEBI:16811 (2)
CHEBI:17126 (2)
CHEBI:17568 (2)
CHEBI:17596 (2)
CHEBI:17712 (2)
CHEBI:17748 (2)
CHEBI:17821 (2)
CHEBI:18186 (2)
CHEBI:18237 (2)
CHEBI:18295 (2)
CHEBI:18344 (2)
CHEBI:25017 (2)
CHEBI:25094 (2)
CHEBI:26271 (2)
CHEBI:27897 (2)
CHEBI:28044 (2)
CHEBI:28300 (2)
CHEBI:30832 (2)
CHEBI:33508 (2)
CHEBI:42534 (2)
CHEBI:7916 (2)

Metabolite Name

Kynurenic acid (2)
(7Z,10Z)-hexadecadienoylcarnitine (1)
(9Z,12Z)-3-hydroxyhexadecadienoylcarnitine (1)
(R)-3-Hydroxybutyric acid (1)
(ÃÂ±)-2-(1-Methylpropyl)-4,6-dinitrophenol (1)
1,11-Undecanedicarboxylic acid (1)
1,3,5-Trihydroxybenzene (1)
10E,12Z-Octadecadienoic acid (1)
12-Hydroxydodecanoic acid (1)
12-Oxo-2,3-dinor-10,15-phytodienoic acid (1)
12-aminododecanoic acid (1)
15-Keto-13,14-dihydroprostaglandin A2 (1)
15-Keto-prostaglandin E2 (1)
16-Hydroxy hexadecanoic acid (1)
16-Methylheptadecanoic acid (1)
1H-Indole-3-carboxaldehyde (1)
2,2-Dimethylsuccinic acid (1)
2,3-Dihydroxybutanedioic acid (1)
2-Hydroxyethanesulfonate (1)
2-Hydroxyvaleric acid (1)
2-Methylglutaric acid (1)
2-Oxovaleric acid (1)
2-hydroxybenzenesulfonic acid (1)
3,3-Dimethylglutaric acid (1)
3-(3,4-Dihydroxy-5-methoxy)-2-propenoic acid (1)
3-Cresotinic acid (1)
3-Hydroxyanthranilic acid (1)
3-Hydroxybenzoic acid (1)
3-Hydroxybutyric acid (1)
3-Hydroxycapric acid (1)

Study type

Transcription profiling by array (839)
RNA-seq of coding RNA (120)
ChIP-seq (101)
ChIP-chip by tiling array (37)
RNA-seq of coding RNA from single cells (33)
Comparative genomic hybridization by array (29)
ChIP-chip by array (27)
Other (22)
Unknown experiment type (13)
RNA-seq of non coding RNA (13)
Genotyping by array (12)
Methylation profiling by high throughput sequencing (11)
Single nucleus RNA sequencing (9)
DNA-seq (8)
Methylation profiling by array (8)
RNAi profiling by array (7)
Transcription profiling by tiling array (6)
RIP-seq (6)
CUT&RUN (6)
High-throughput sequencing (5)
Animal - High-throughput sequencing (5)
Hi-C (5)
ScATAC-seq (5)
Animal - Single-cell sequencing (4)
ATAC-seq (4)
Cell line - High-throughput sequencing (3)
RNA-seq of total RNA (3)
Plant - High-throughput sequencing (2)
Transcription profiling by RT-PCR (2)
4C (2)

Release Date

2013 (170)
2010 (148)
2015 (139)
2014 (129)
2012 (125)
2008 (109)
2016 (95)
2011 (91)
2022 (80)
2009 (71)
2021 (58)
2020 (50)
2023 (40)
2007 (38)
2018 (36)
2005 (36)
2025 (35)
2026 (32)
2006 (31)
2017 (30)
2024 (27)
2019 (18)
2004 (11)
2003 (6)

Lab affiliation

CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. (1)
CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. (1)
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada. (1)
Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute Third floor, room 368 The University of Melbourne Victoria 3010 Australia (1)
Department of Biochemistry and Molecular Biology, Mitochondria lab, Monash University, Clayton 3800, Australia (1)
Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine (1)
National Chromatography Research and Analysis Center,Department of Biology,Dalian Institute of Chemical Physics (1)
School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD, Australia, 4072 (lab head) (1)
Tea Research Institute (CAAS), China (1)

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Expression data from BNL CL.2 liver cells when cultured with iron, RAW 264.7 macrophages or both

We found that co-culturing BNL CL.2 liver cells with RAW 264.7 macrophages increased IRP binding in the first. To further investigate this modulation we investigated the gene expression profile in BNL CL.2 cells cultured alone, with iron, with RAW 264.7 macrophages or in the presence of both iron an...

ORGANISM(S): Mus musculus

2016-10-22 | E-GEOD-32090 | biostudies-arrayexpress

Microarray analysis of CL-20 reversible neurotoxicity in the earthworm Eisenia fetida

The earthworm Eisenia fetida is one of the most used species in standardized soil ecotoxicity tests. Endpoints such as survival, growth and reproduction are ecologically relevant but provide little mechanistic insight into the toxicity pathways, especially at the molecular level. To better understan...

ORGANISM(S): Eisenia fetida

2009-10-14 | E-GEOD-18536 | biostudies-arrayexpress

Transcription profiling of C. kokaiensis CL, INT, and CH flowers on an Arabidopsis array

The annual cleistogamous herb Cardamine kokaiensis is an endemic plant along the Kokai River in Japan. We examined the differences in gene expression patterns among cleistogamous (CL), intermediate (INT), and chasmogamous (CH) flower by cross-species microarray analysis using an Arabidopsis thaliana...

ORGANISM(S): Cardamine sp. SIM-2007

2008-06-18 | E-GEOD-9799 | biostudies-arrayexpress

A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme

The histone variant H2A.Z plays key roles in gene expression, DNA repair, and centromere function. H2A.Z deposition is controlled by SWR-C chromatin remodeling enzymes that catalyze the nucleosomal exchange of canonical H2A with H2A.Z. Here we report that acetylation of histone H3 lysine 56 (H3-K56A...

ORGANISM(S): Saccharomyces cerevisiae W303

2013-04-15 | E-GEOD-43935 | biostudies-arrayexpress

Cultured chicken embryonic hepatocytes (CEH) exposed to linear PFOS (L-PFOS) or technical-grade PFOS (T-PFOS)

Recently it was discovered that the perfluorooctane sulfonate (PFOS) detected in wildlife, such as fish-eating birds, had a greater proportion of linear PFOS (L-PFOS) than the manufactured technical product (T-PFOS), which contains linear and branched isomers. This suggests toxicological studies bas...

ORGANISM(S): Gallus gallus

2011-10-28 | E-GEOD-33291 | biostudies-arrayexpress

Bipolar Membrane Electrodialysis for Direct Conversion of L-Ornithine Monohydrochloride to L-Ornithine.

Not available

S-EPMC10488261 | biostudies-literature

Global metabolomics of fireflies (Coleoptera: Lampyridae) explore metabolic adaptation to fresh water in insects

Aquatic insects are well-adapted to freshwater environments, but metabolic mechanisms of such adaptations, particularly to primary environmental factors (e.g., hypoxia, water pressure, dark light and abundant microbes), are poorly known. Most firefly species (Coleoptera: Lampyridae) are terrestri...

2022-10-03 | MTBLS4987 | MetaboLights

Transcription profiling of C. elegans IG274 wt frIs7 and IG339 nipi-1(fr1) frIs7 after infection with Dreshmeria coniosporia

1.Sample Growth Conditions protocols
Eggs from IG274 wt; frIs7 and IG339 nipi-1(fr1); frIs7 worms cultivated at 25Ã‚Â°C were allowed to hatch in the absence of food at 25Ã‚Â°C for 16 hours. Synchronised larvae were transferred to NGM agar plates lawned with OP50 and cultivated at 25°C for 48 hou...

ORGANISM(S): Caenorhabditis elegans

2009-10-29 | E-MEXP-1364 | biostudies-arrayexpress

Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C

Small, non-coding RNAs control gene expression post-transcriptionally and play important roles in virus-host interactions. Within the liver, the microRNA (miRNA) miR-122 is essential for replication of hepatitis C virus (HCV), while repression of miR-148a by hepatitis B virus (HBV) may enhance tumor...

ORGANISM(S): Homo sapiens

2014-12-18 | E-GEOD-57381 | biostudies-arrayexpress

Low input Hi-C datasets for a diffuse large B-cell lymphoma sample, healthy control human B-cells and mouse embryonic stem cells

In this experiment, we've examined chromatin conformation of OG2 (B6; CBA-Tg(Pou5f1-EGFP)2Mnn/J; stock number 004654) mouse stem cells cultured as described in (Shi et al., 2008), using different amounts of starting cells. We performed a modified in situ Hi-C protocol for 6 samples digested with Mbo...