Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing of MCF7 cells after vinigrol 6 hours treatment

ABSTRACT: This study compares the gene expression level in four cancer cell lines before and after vinigrol treatment. The Lexogen QuantSeq 3'mRNA-seq library kit or Hieff NGS MaxUp II Dual-mode mRNA Library Prep Kit for Illumina MaxUp II was used to prepare the RNA-seq libraries in this study. We identified the dysregulated genes during this progress and explored the potential mechanism of vinigrol induced cell death in breast cancer cells. Overall design: MCF7-ADR, ,MDA-MB-231 and T47D cells treated with vinigrol (50 micromoles) for 6 hours compared with the DMSO group.

ORGANISM(S): Homo sapiens

PROVIDER: GSE180462 | GEO | 2022/07/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome 3' end profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination.

Project description:We performed mRNA 3'end sequencing experiments on three biological replicates of HeLa cells depleted of MATR3, PTBP1/2, controls, or combined depletion of MATR3/PTBP1/2. Cells were fractionated into cytoplasmic and nuclear RNAn and only the nuclear RNA was used. Library preparation was done with the QuantSeq library kit (Lexogen) according to manufacturer’s recommendations. Replicates 1 and 2 were prepared with the QuantSeq forward library kit, replicates 3 and 4 with the QuantSeq reverse library kit. All libraries were sequenced on Illumina HiSeq2 machines in a single-end manner with a read length of 100 nt.

2018-05-01 | E-MTAB-6287 | biostudies-arrayexpress

QuantSeq-Reverse analysis of total RNA extracted for healthy and osteoarthritic human articular cartilage

Project description:The main aim was to determine how polyadenylation site usage is affected by osteoarthritis. Age matched tissue samples were obtained from both healthy individuals and those with late stage osteoarthritis, total RNA was isolated and then QuantSeq Reverse library produced using commercial kit (Lexogen) before sequencing

2022-10-01 | E-MTAB-12184 | biostudies-arrayexpress

RNA sequencing of young versus aged endothelial cells

Project description:Freshly dissected Thymus, Kidney, and Spleen from young and aged mice were subjected to collagenase digestion to prepare single-cell suspension for the isolation of endothelial cells. Endothelial cells form the single-cell suspension was isolated using a magnetic bead-based separation method using CD144 and Endomucin antibody. RNA from 150,000 cells from each group was isolated using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instructions. The library preparation was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina.

2021-01-23 | E-MTAB-8941 | biostudies-arrayexpress

RNA sequencing of blood brain barrier spheroids exposed to either Neisseria meningitidis or Borrelia bavariensis in in vitro conditions

Project description:Neisseria meningitidis and Borrelia bavariensis are the causative agents of invasive meningococcal disease and Lyme neuroborrelosis. Before infecting the brain parenchyma the bacterial pathogens should cross the human blood-brain barrier (BBB). To understand the response of BBB against the invading pathogens, in vitro BBB spheroid model was generated by co cultivating human brain microvascular endothelial cells, pericytes and astrocytes in low adhesion conditions. Spheroids (N= 36) were infected with either N. meningitidis (6 x 10e4, MOI 1:4) or B bavariensis(1.5 x 10e5, MOI 1:10) for 3h. Two separate control groups of spheroids (N=36) without any infection were included in the study. After 3h of treatment (infection/no infection), 12 spheroids were pooled to form one biological sample and such 3 biological replicates per treatment were sampled for total RNA extraction. Thereafter, 12 cDNA libraries were prepared using QuantSeq FWD 3’mRNA Library Prep Kit (Lexogen). Second strand of cDNA library was synthesized using the UMI Second Strand Synthesis Mix (USS, Lexogen) containing 6 nucleotides long Unique Molecular Identifiers (UMIs). The double stranded cDNA libraries were amplified in 17-19 PCR cycles using i5 Unique Dual Indexing Add-on Kit (Lexogen). Illumina NextSeq 500 was employed to sequence the libraries having a read lengths of single-end 75 bp producing about 10 million reads per library. To carryout gene expression analysis, Bioconductor R-package - DESeq2 v1.20.0 (Love et al., 2014) was used where in, featureCounts tool v1.6.3 (Liao et al., 2013) was used to enumerate the genes. A minimum threshold of adjusted p-value < 0.05 and log2fold-change (log2FC) = ± 1 was set to considered the gene as differentially expressed (DEG).

2023-10-31 | E-MTAB-13401 | biostudies-arrayexpress

3' mRNA-seq of neurites and soma isolated from mESC-derived neurons

Project description:3' mRNA-seq was performed with QuantSeq 3' mRNA-Seq kit (Lexogen 015) according to the manufacturer’s recommendations. 3' mRNA-seq was done in biological triplicates (soma) or duplicates (neurites), using 260 ng of total RNA from neurites or soma of mESC-derived neurons per sample. Libraries were pooled and sequenced on Illumina NextSeq 500 system with a single-end 150-cycle run.

2019-01-12 | E-MTAB-7251 | biostudies-arrayexpress

PAS-CLASH (PolyA Site-Crosslinking, Ligation and Sequencing of the Hybrid) analysis to detect RNA-RNA interaction at poly(A) site region

Project description:In an attempt to discover potential RNA-RNA interactions in mRNA 3’ processing regulation, we developed PAS-CLASH (PolyA Site-Crosslinking, Ligation and Sequencing of the Hybrid) method, which combines reported CLASH and poly(A) site sequencing protocols. Briefly, HeLa cells were treated with AMT, or without AMT as control, and irradiated at 365 nm for crosslinking. Following nuclear RNA fragmentation and purification, the potential proximate RNAs/PASs were ligated on the oligo d(T)25 beads, hybrids were reverse crosslinked and amplified with the QuantSeq Rev 3' mRNA sequencing library prep kit (Lexogen, Cat. 016.24) and sequenced with Hiseq, producing 150 bp paired end reads.

2019-01-22 | GSE125398 | GEO

Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration

Project description:The goal of this study is to use RNA-seq to investigate the molecular mechanisms by which REST inhibition regulates corticalspinal axon regeneration. To achieve this goal, cortical motor neurons from adult wild-type (WT) and REST conditional knockout (cKO) were purified at 1, 3, 7 days following spinal cord injury (SCI) or sham operation. RNA-seq libraries for cortical motor neurons were prepared with the QuantSeq mRNA-Seq library prep kit FWD for Illumina (Lexogen) and sequenced using HiSeq4000 (Illumina). Sequenced reads were mapped to reference genome (mm10) using STAR, and count level data were quantifed using Salmon. Differential gene expression analysis was performed using limma voom.

2022-05-23 | GSE141583 | GEO

RNA-Seq of BRQ-treated and control B16F10 cells

Project description:B16F10 cells treated with DMSO or BRQ were collected and then the total RNA was isolated. After removal of the remaining genomic DNA, mRNA was purified from total RNA using polyT and then fragmented with 10× RNA fragmentation buffer and the RNA-seq library was constructed using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit and was sequenced.

2023-11-01 | GSE245151 | GEO

RNA-Seq of GB2-treated and untreated RAW264.7 cells

Project description:RAW264.7 cells treated with GB2 or not were collected and then the total RNA was isolated. After removal of the remaining genomic DNA, MRNA was purified from total RNA using polyT and then fragmented with 10x RNA fragmentation buffer and the RNA-seg library was constructed using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit and was sequenced.

2024-12-20 | GSE251808 | GEO

RNA-Seq of GB2-treated and untreated MC38 tumors

Project description:MC38 tumors from C57BL/6 mice treated with GB2 or PBS were collected and then the total RNA was isolated. After removal of the remaining genomic DNA, MRNA was purified from total RNA using polyT and then fragmented with 10x RNA fragmentation buffer and the RNA-seg library was constructed using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit and was sequenced.

2024-12-20 | GSE251810 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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