Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

3'mRNA-Seq of drug-tolerant medulloblastoma cell lines.

ABSTRACT: Stable cisplatin- and vincristine-tolerant Group 3 and SHH cell lines were generated by continuous drug exposure with dose escalation to identify mechanisms driving resistance to standard-of-care medulloblastoma therapy. Next-generation sequencing revealed a vastly different transcriptomic landscape following chronic drug exposure, including a drug-tolerant gene expression signature, common to all sequenced drug-tolerant cell lines.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Louisa Taylor

PROVIDER: E-MTAB-12686 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNAseq of two medulloblastoma cell lines (ONS-76 and HDMB-03) grown in 3D hydrogel culture

Project description:Two medulloblastoma cell lines (ONS-76 and HDMB-03) were grown in 3D hyaluronan hydrogels for three weeks. We observed nodules forming showing different behavior and wanted to evaluate if these different nodules (slow vs fast vs non-growing, migrating and invading cells) are also characterised by different gene expression patterns. We performed this experiment on a SHH (ONS-76) and on a group 3 MB (HDMB-03) cell line to compare if certain subpopulations would be unique for the subgroups.

2023-02-23 | E-MTAB-12591 | biostudies-arrayexpress

Trex1 knock out in cancer cell lines

Project description:We performed bulk RNA-seq on cell lines with and without knock out of the Trex1 gene.

2024-03-12 | E-MTAB-13815 | biostudies-arrayexpress

Bulk RNA-seq OT-I Cd8 T cells

Project description:To better understand the mechanisms downstream of IL-27 signaling, we performed RNA sequencing on repetitively stimulated OT-I T cells treated with IL-27.

2024-12-06 | E-MTAB-14580 | biostudies-arrayexpress

Bulk RNA-seq of Cd4 T cells from mice with MC38 tumors

Project description:To understand the role of IL-27 receptor agonism in tumor regression in mice, we examined Cd4 T conventional T cells and Tregs from tumor and lymph node.

2024-12-06 | E-MTAB-14581 | biostudies-arrayexpress

mRNA sequencing of rat hearts treated chronically with rofecoxib or its vehicle

Project description:We reported previously that chronic treatment with the Cyclooxygenase-2 inhibitor, rofecoxib, increased acute mortality in rats exposed to ischemia/reperfusion injury (I/R). This manifestation of hidden cardiotoxicity was attributed to the proarrhythmic effect of the drug on the ischemic heart. However, rofecoxib also had beneficial effects on ischemic injury, manifesting as decreased infarct size. In the present study, we aimed to identify molecular changes caused by chronic rofecoxib treatment in the heart. Rats were treated with 5.12 mg/kg rofecoxib or its vehicle for four weeks. Messenger RNA (mRNA), microRNA (miRNA) deep sequencing data, and proteomic datasets of left ventricular tissue samples were used for an unbiased differential expression analysis followed by in silico molecular network analysis and experimental target validation. Using mass spectrometry and filtering criteria, 26 proteins were identified that exhibited pronounced changes in protein expression or phosphorylation due to chronic rofecoxib treatment. The transcriptomic analysis showed mild alterations in the heart´s mRNA- and miRNA expression. The posttranscriptional regulation of mRNAs by miRNAs did not result in differential protein expression. This is the first demonstration that chronic rofecoxib treatment affects posttranslational modification and expression of several proteins in the heart. These are potential off-target effects that could account for the hidden cardiotoxic and/or cardioprotective effects of rofecoxib.

2024-10-30 | E-MTAB-13913 | biostudies-arrayexpress

mRNA-Seq and 3'mRNA-Seq analyses of A2Lox mouse embryonic stem cells treated with control siRNA or siRNAs against Srrt or Ncbp1

Project description:The experiment was carried out to characterize new biological functions of components of the cap-binding complex. A2Lox mouse embryonic stem cells were transfected with Srrt- or Ncbp1-specific siRNA or a non-targeting siRNA control. Total RNAs were extracted at 48 hours post transfection and QC'd. For mRNA-Seq analyses, purified total RNAs were hybridized with oligo(dT) magnetic beads to isolate the poly(A) RNA fraction. Stranded mRNA sequencing libraries were then prepared using the Illumina TruSeq Stranded mRNA Library Kit and sequenced using an Illumina HiSeq 2500 instrument. For 3'mRNA-Seq, sequencing-ready libraries were produced using a QuantSeq 3' mRNA-Seq Library Prep Kit REV and sequenced using an Illumina HiSeq 2500 instrument.

2019-11-27 | E-MTAB-7626 | biostudies-arrayexpress

Role and dysregulation of miRNA in patients with Parkinson’s disease

Project description:Parkinson’s disease (PD) is the most common movement disorder in the aging population, with an estimated prevalence of 1% of people above 60 years old. More recently, PD risk genes, have been found to be regulated by the small non-coding RNAs, (microRNAs or miRNAs), and, as such, may contribute to PD development through a direct regulation on the mitochondrial and immune pathways. Many of these are influenced by epigenetic mechanisms, among which ones mediated by, miRNAs, that regulate gene expression at a post transcriptional level by binding to their 3′ un-translated region (3′ UTR) of target messenger RNAs (mRNAs) inducing mRNA degradation and translational repression. This study aimed to identify and characterize miRNA to evaluate their possible deregulation in PD patients compared to CRTL. In addition, we investigated how specific miRNAs are able to target genes and, thus, to modulate their functions in PD patient. Small RNA expression profiling was performed by next-generation sequencing in PD patients and CTRL after filtered out low-quality reads and trimming the adaptors. The obtained high-quality reads were aligned against the human genome reference.

2023-09-01 | E-MTAB-12087 | biostudies-arrayexpress

Drug tolerant persister cells of EGFR-mutant cell line under kinase-inhibitor combination

Project description:Drug tolerant persister cells of EGFR-mutant PC9 cell lines surviving treatment with kinase inhibitor combination. Cells were treated with combination of erlotinib, osimertinib, trametinib and dasatinib and surviving cells were harvested for RNA extraction. 3' UTR RNA-seq profiles were compared to parental control cells and to outgrowing cells after treatment had been removed

2023-06-30 | E-MTAB-13045 | biostudies-arrayexpress

Proteomes and Histone Crotonylation Analysis Reveals the Importance of Crotonylation Low Temperature in Chrysanthemum

Project description:Chrysanthemum is a garden plant with good economic benefit and high ornamental value. Chrysanthemum in the key period of flowering in autumn and winter, vulnerable to cold damage, affecting the normal growth of the chrysanthemum plant and even death. little is known regarding the study of histone crotonylation in plant cold response. In this study, we first obtained reference chrysanthemum transcriptome data via RNA sequencing. Next, we quantitatively investigated the chrysanthemum proteome, crotonylation, and the association between them in chrysanthemum following low temperature. In total, 365669 unigenes, 6693 proteins and 2017 crotonylation sites were quantified under low temperature stress. There were 24631 up-regulated and 22648 down-regulated unigenes (absolute log2-fold change > 1 and P value<0.05), 393 up-regulated and 500 down-regulated proteins using a 1.2-fold threshold (P<0.05). The lysine crotonylation mainly influenced in photosynthesis, ribosome, antioxidant enzyme and ROS system. In the process of low temperature, 61 lysine crotonylation sites in 89 proteins were up-regulated and 87 lysine crotonylation sites in 72 proteins are down-regulated (1.2-fold threshold, P<0.05).

2021-01-04 | PXD010297 | Pride

Whole Transcriptome Sequencing of Cervical Adenocarcinoma

Project description:The raw data consists of Transcriptome sequencing of 24 tumor samples and 5 normal samples of cervical adenocarcinoma samples

2022-02-11 | E-MTAB-9281 | biostudies-arrayexpress