Gem - OmicsDI

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Instrument Platform

Illumina NovaSeq 6000 (254)
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Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (4)
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DNBSEQ-G400 (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 (2)
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UNIPROT ID/AC

Q01813 (2)
P43490 (2)
P17858 (2)
P21439 (2)
P05062 (2)
P09972 (2)
P04075 (2)
P07738 (2)
P00338 (2)
P07195 (2)
P14618 (2)
P04406 (2)
P30613 (2)
P06744 (2)
P06733 (2)
P09104 (2)
P13929 (2)
P08237 (2)
O14556 (2)
P00558 (2)
P07205 (2)
P18669 (2)
P60174 (2)
Q8CQ79 (1)
A0A0H2VIH0 (1)
Q8CPG7 (1)
Q8CPZ7 (1)
Q8CS47 (1)
Q8CSX6 (1)
Q8CMM3 (1)

CHEBI ID

CHEBI:16335 (62)
CHEBI:16235 (61)
CHEBI:16708 (61)
CHEBI:17748 (61)
CHEBI:17368 (61)
CHEBI:16750 (61)
CHEBI:17562 (61)
CHEBI:17596 (61)
CHEBI:17256 (60)
CHEBI:29101 (59)
CHEBI:17154 (59)
CHEBI:16842 (59)
CHEBI:17158 (59)
CHEBI:18191 (59)
CHEBI:18421 (59)
CHEBI:29033 (59)
CHEBI:17544 (59)
CHEBI:15343 (59)
CHEBI:16189 (59)
CHEBI:16240 (59)
CHEBI:16526 (59)
CHEBI:17568 (59)
CHEBI:16016 (59)
CHEBI:18107 (59)
CHEBI:17268 (59)
CHEBI:15377 (59)
CHEBI:15379 (59)
CHEBI:17790 (58)
CHEBI:15927 (58)
CHEBI:16865 (58)

Metabolite Name

Adenosine (3)
Guanine (3)
Diflufenican (2)
Amitraz (2)
Bentazone (2)
4-Methylumbelliferone (2)
Naringin (2)
Ciprofloxacin (2)
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Nebularine (2)
Fluazifop (2)
AMP (2)
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Rutin (2)
Oxaprozin (2)
Rosmarinic acid (2)
Cystine (2)
Choline (2)
Gamma-Glutamylleucine (2)
Taurine (2)
Gentisic acid (2)
Niacinamide (2)
Pantothenic acid (2)
Cytosine (2)
NADH (2)
Adenine (2)
Guanosine (2)

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2012 (2)

Modelling Approach

Constraint-based model (62)
Metabolic network (2)
Other (2)
Steady-state model (1)
Differential equation model (1)
Ordinary differential equation model (1)

Study status

Completed (1)

Lab affiliation

State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China (2)
Advanced Water Management Centre, The University of Queensland (1)
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland (1)
Department of Geoscience, University of Calgary (1)
Department of Medicine, University of California San Diego, La Jolla, California 92093 (1)
Department of Pharmaceutical Sciences, School of Pharmacy, University at Buffalo, Buffalo, New York, United States (1)
Department of Pharmaceutical Sciences, University at Buffalo, NY, USA (1)
Northwestern University Feinberg School of Medicine (1)
Shenyang Agricultural University (1)
The Third Medical Center, Chinese PLA General Hospital (1)
University at Buffalo (1)

Keyword

Gemcitabine (1)

IsPrivate

False (105)

Model Flag

Non Kinetic (39)

Submitter Keywords

FROG (23)
Not Peer Reviewed (11)
Manuscript Accepted (1)
COVID-19 (1)

Classification

protozoa (1)

Study type

RNA-seq of coding RNA from single cells (336)
Transcription profiling by array (82)
RNA-seq of coding RNA (34)
Single nucleus RNA sequencing (23)
ChIP-seq (15)
ScATAC-seq (10)
Human - Single-cell sequencing (5)
Comparative genomic hybridization by array (5)
Cell line - Single-cell sequencing (4)
Animal - Single-cell sequencing (4)
Cell line - High-throughput sequencing (4)
Methylation profiling by high throughput sequencing (4)
RNA-seq of non coding RNA (4)
Unknown experiment type (3)
Human - High-throughput sequencing (3)
DNA-seq (3)
Differential (2)
Genotyping by array (2)
ATAC-seq (2)
Other (2)
RNA-seq of total RNA (2)
RAN-seq of total RNA from single cells (1)
Baseline (1)
RNA-seq of non coding RNA from single cells (1)
ChIP-chip by tiling array (1)
High-throughput sequencing (1)
RNAi profiling by array (1)
MicroRNA profiling by array (1)
Methylation profiling by array (1)
Genotyping by high throughput sequencing (1)

Release Date

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2011 (23)
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2008 (17)
2007 (10)
2006 (7)
2004 (3)
2003 (2)
2002 (2)
2005 (1)
2001 (1)
2000 (1)

Location

United States (1)

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GEM-CESAR

PRJEB72353 | ENA

Identifying actionable targets through integrative analyses of GEM model and human prostate cancer profiling (Illumina)

Here we profile prostate cancers derived from GEM models of prostate cancer representative of human prostate cancer Total RNA was isolated from established prostate cancers in 3 GEM models of prostate cancer - PB-MYC, Pten-/-, Pten-/- p53-/-

ORGANISM(S): Mus musculus

2015-02-20 | E-GEOD-61379 | biostudies-arrayexpress

Establishment of pancreatic cancer cells spectral library based on data-independent acquisition strategy and the phenotype analysis of pancreatic cell lines of the sensitivity and resistance of gemcitabine

Based on data-independent acquisition (DIA)-mass spectrometry (MS) proteomics, we first established a high-coverage human pancreatic cells spectrum library. Furthermore, analyzed the sensitivity and drug resistance phenotypes to gemcitabine (GEM).

ORGANISM(S): Homo sapiens (Human)

2022-05-31 | PXD031028 | Pride

Gene expression profiling of gemcitabine sensitive BxPC-3 pancreatic cancer cell lines and their derived resistant subclones, Bx-GEM

This experiment describes the differential gene expression between parental gemcitabine-sensitive BxPC-3 cells and their resistant subclones, Bx-GEM. To select for the resistant subclones, parental BxPC-3 cells were treated with increasing concentrations of gemcitabine (10, 25, 50, 100 and 200 nM) f...

ORGANISM(S): Homo sapiens

2017-01-20 | E-MTAB-4901 | biostudies-arrayexpress

Geminin knockdown in embryonic stem cell-derived neural precursors

Regulating the transition from lineage-restricted progenitors to terminally differentiated cells is a central aspect of nervous system development. Here, we investigated the role of the nucleoprotein Geminin in regulating neurogenesis at a mechanistic level during both Xenopus primary neurogenesis a...

ORGANISM(S): Mus musculus

2012-12-06 | E-GEOD-39657 | biostudies-arrayexpress

Identifying actionable targets through integrative analyses of GEM model and human prostate cancer profiling [Agilent]

Here we prolife prostate cancers derived from GEM models of prostate cancer representative of human prostate cancer Total DNA was isolated from established prostate cancers in 4 GEM models of prostate cancer - PB-MYC, Pten-/-, Pten-/- p53-/-, Pten-/- Rosa26-ERG, and 3 cell lines derived from GEM mod...

ORGANISM(S): Mus musculus

2015-02-20 | E-GEOD-61382 | biostudies-arrayexpress

K562+mESC 10X Chromium Next GEM 3'

Single cell sequencing with 10X Chromium Next GEM 3' of K562 and mESC cells

PRJEB67544 | ENA

Gene expression of VPA and GEM

Background: Histone deacetylase (HDAC) is strongly associated with epigenetic regulation and carcinogenesis, and its inhibitors induce the differentiation or apoptosis of cancer cells. Valproic acid (VPA) is one of the clinically available HDAC inhibitors. We investigated the anticancer effects of V...

ORGANISM(S): Homo sapiens

2011-02-09 | GSE27036 | GEO

Haiman2025 - RBC-GEM v1.2.0

Initial submission of RBC-GEM genome-scale metabolic model, version 1.2.0.

2025-04-07 | MODEL2410170001 | BioModels

microRNA profiling by array of gemcitabine sensitive BxPC-3 pancreatic cancer cell lines and their derived resistant subclones, Bx-GEM

This experiment describes the differential microRNA expression between parental gemcitabine-sensitive BxPC-3 cells and their resistant subclones, Bx-GEM. To select for the resistant subclones, parental BxPC-3 cells were treated with increasing concentrations of gemcitabine (10, 25, 50, 100 and 200 n...

ORGANISM(S): Homo sapiens

2017-01-20 | E-MTAB-4927 | biostudies-arrayexpress

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