Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single Cell RNA-Seq data for Cancer Stem Like Reversal Project

ABSTRACT: Primary breast cancer samples were obtained from malignant pleural effusions or ascites after completely red blood cells depletion. For single cell RNA sequencing, frozen vials were thawed and viable breast cancer cells were obtained after depletion of dead cells and CD45+ cells. The purifed patient cells were cultured in Renaissance medium (3D) and treated with chemotherapy (doxorubicin 0.1 µM, carboplatin 0.1mM, paclitaxel 1µM) for 72 hours, and then replaced with Renaissance medium containing DMSO/belinostat (1µM) for 72 hours incubation. The cells were collected, purified with Dead Cell Removal Kit, and subjected to ICELL8® Single-Cell System.

ORGANISM(S): Homo sapiens

PROVIDER: GSE147326 | GEO | 2020/12/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA sequencing of small non-coding RNAs in murine subcutaneous adipose tissue

Project description:Mice overexpressing a kinase dead AMPKa2 subunit or control were exercised 6.5 weeks and sacrifised 24 hours after last exercise bout. Total RNA from subcutaneous adipose tissue were isolated and small RNAs were purifed from this.

2020-08-24 | GSE115408 | GEO

transcriptomic analysis of the effects of low levels of atrazine and by-products-Molecular analysis of signal transduction mechanisms involved in plant – organic pollutant interactions.

Project description:au15-04_xeno - transcriptomic analysis of the effects of low levels of atrazine and by-products - Identification of xenobiotic direct sensing and of low chemical stress transduction networks in Arabidopsis thaliana. - Seeds of Arabidopsis thaliana (Columbia ecotype, Col-0) were surfaced-sterilized in bayrochlore/ethanol (1/1, v/v), rinsed in absolute ethanol and dried overnight. Germination and growth were carried out under axenic conditions in square Petri dishes. After seeds were sowed, Petri dishes were placed in the dark at 4 °C for 72 h in order to break dormancy and homogenize germination, and were then transferred to a control growth chamber at 22 °C/20 °C under a 16 h light (6000 lux)/8 h dark regime. Growth medium consisted of 0.8% (w/v) agar in Hoagland basal salt mix (H2395, Sigma-Aldrich) adjusted to pH 6. After 13 days of growth under optimal conditions, seedlings were transferred to fresh growth medium containing pesticides during 24 h (Control, Atrazine 1µM, Hydroxyatrazine 1µM or Desethylatrazine 1µM). Then control and treated seedlings were harvested and ground in liquid nitrogen until RNA extraction by RNeasy kit (Qiagen) and DNase digestion. RNA was extracted on at least 2 independent biological replicates of 30 pooled plantlets.

2016-11-01 | GSE88788 | GEO

Combinatorial Ixazomib and Belinostat Therapy Induce Nuclear Factor Erythroid 2-Related Factor 2 (NRF2)-Dependent Apoptosis in Hodgkin and T-cell Lymphoma

Project description:Ixazomib has documented pre-clinical activity in T cell (TCL) and Hodgkin (HL) lymphoma models with transcriptomic analyses predicting synergistic activity in combination with histone deacetylase (HDAC) inhibition. In the present study, we determined the mechanistic basis for synergism with ixazomib in combination with the HDAC inhibitor, belinostat, in HL and TCL cells lines (ixazomib-sensitive and -resistant clones) and primary tumor cells. In ixazomib-treated TCL and HL cells, we observed induction of proteasomal gene expression and NRF2 as a prominent upstream regulator. Ixazomib treatment in TCL and HL cells resulted in transient inhibition followed by full recovery of proteasomal activity within 72 hours. Furthermore, transcriptomic analysis following belinostat treatment resulted in downregulation of both NRF2 and proteasomal gene expression (validated by qPCR) without direct impact on proteasomal activity in Jurkat and L428. In addition, CRISPR/Cas9 mediated knockdown of NRF2 in Jurkat cells resulted in a significant decrease in cell viability with ixazomib compared with untreated control cells. Using transcriptomic and proteosomal activity evaluation of ixazomib, belinostat or ixazomib+belinostat treated cells, we observed that NRF-2, proteasome gene expression and functional recovery were abrogated by the combination. We also confirmed that ixazomib/belinostat resulted in synergistic activity in ixazomib-sensitive and -resistant cell lines and primary cells. Altogether, these results suggest that the synergistic activity of ixazomib and belinostat is mediated via inhibition NRF2-dependent proteasomal recovery and extended proteasomal inhibition culminating in increased cell death. Further investigation is warranted to determine the full biological role for NRF2 as a response modifier in proteasomal targeted therapies.

2019-04-01 | GSE126768 | GEO

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [Pro-seq]

Project description:To characterize transcription throughout the HCMV infection, paired-end PRO-Seq was performed on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h, 12 h, 24 h, 48 h, and 72 h using the TB40/e strain. Cells were treated with 1µM flavopiridol 1 hour prior to isolation. Additionally, PRO-Cap was performed on untreated HFFs after 72 h of infection. Each experiment was performed with adapters containing 8 nt of random sequence flanking both ends (16 total bases of randomness) to enable deduplication.

2022-02-17 | GSE185762 | GEO

Effect of cortisol on S. Typhimurium parental strain and an isogenic scsA mutant

Project description:S. Typhimurium 112910a parental strain and an isogenic ΔscsA strain were grown to stationary phase in SPI2 inducing minimal medium (MM5.8 - Erikkson et al., 2006 Inf & Imm., 74:1243) with or without supplementation with 1µM cortisol

2014-02-28 | GSE55430 | GEO

scRNA-Seq from stroma vascular fraction of abdominal and gluteofemoral subcutaneous white adipose tissue

Project description:SVF was isolated from ABD and GF-adipose tissue biopsies by collagenase digestion and centrifugation, from 5 healthy women (38yo ±4.4; 31.8kg/m-2 ±3.12; WHR 0.86 ±0.05). After isolation, cells were counted with a Countess II automated cell counter (Thermofisher Scientific). Single cell suspension (56K/mL) was distributed into eight wells of a 384-well source plate (Takara Bio USA, San Jose, CA) and dispensed onto a iCELL8 350v Chip (Takara Bio USA) using an iCELL8 MultiSample NanoDispenser (Takara Bio USA). We distributed the ABD and GF-SVF of each subject on the same chip. The method used was described in [6]. In brief, mRNA from single cells were isolated, converted to full-length cDNA prior to unbiased amplification of 3’ and 5’ ends using SMART-Seq® ICELL8® Application Kit (Takara Bio, USA). Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol and 150bp paired-end sequencing was performed on an Novogene HiSeqX instrument.

2024-02-23 | GSE255996 | GEO

Expression data from lung SCC treated with DMSO and PXD101

Project description:We used microarrays to detail the global programme of gene expression in lung SCC cells treated with belinostat, a pan-HDAC inhibitor. The primary focus of this work is to investigate the efficacy of belinostat on lung SCC cells. Our phosphoproteomic profiling analyses revealed the downregulation of MAPK signaling pathway upon drug treatment, together with the induction of apoptosis. While HDAC inhibition generally affects transcription, the mechanism of SOS/MAPK downregulation was therefore proposed to be affected at the transcriptomic level. However, genes related to MAPK pathway were not significantly regulated upon belinostat treatment, whereas ubiquitin-proteasome gene signature was affected. This supports an indirect mechanism of epigenetic regulation on MAPK signaling that should be explored further.

2017-08-31 | GSE85979 | GEO

Mapping the soluble human leukocyte antigen peptidome of pleural effusions reveals lung and tumor-associated antigens

Project description:Soluble HLA (sHLA) molecules released to the plasma, carry their original peptide cargo and provide insight into the protein synthesis and degradation schemes of their source cells and tissues. Other body fluids, such as pleural effusions, may also contain sHLA-peptide complexes, and can potentially serve as a source of tumor antigens since these fluids are drained from the tumor microenvironment. Thus, we developed a methodology for purifying and analysing large pleural effusion sHLA class I peptidomes of patients inflicted with malignancies or benign diseases. The cleared pleural fluids, the cell pellets present in the pleural effusions, and the primary tumor cells cultured from cancer patients’ effusions, were used for immunoaffinity purification of the HLA molecules. The recovered HLA peptides were analyzed by capillary chromatography coupled to tandem mass spectrometry and the resulting LC-MS/MS data was analyzed with the MaxQuant software tool. Large HLA peptidomes were obtained by the analysis of the pleural effusions. The majority of peptides identified from the pleural effusions were defined as HLA ligands that fit the patients’ HLA consensus sequence motifs. The membranal and soluble HLA peptidomes of each individual patient were somewhat similar to each other. Many of the HLA peptides were derived from known tumor-associated antigens, lung-related proteins, and VEGF pathway proteins. Thus, the pleural effusion HLA peptidome of patients with malignant tumors can serve as a rich source of biomarkers for tumor diagnosis and personalized immunotherapy.

2022-05-25 | PXD027766 | Pride

Phosphoproteome of PINK1 in HEK293 cells

Project description:triple SILAC phosphoproteomics experiment of Flp-In T-Rex HEK293 cells stably expressing either FLAG empty, PINK1-FLAG Kinase dead or PINK1-FLAG wild type were grown in ‘light’ (K0R0), ‘medium’ (K4R6) and ‘heavy’ (K8,R10) SILAC media, respectively.

2015-09-16 | PXD002127 | Pride

Leu Effect on Cultured Human Liver Cell Lines

Project description:The transcript profiles were measured using total RNAs from low (0.1mM) and high (2.0mM) treated THLE-3 cells across 5 time points. Keywords: time-course

2005-03-11 | GSE2386 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data