Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human gastric cancer cell line AGS treated with Capsaicin against DMSO

ABSTRACT: Capsaicin has previously been demonstrated to exhibit anti-tumor effect in various cancer type. However, the deep biological function and molecular mechanism of capsaicin was still uncertain. In this research, we used high-throughput RNA sequencing to unveil the potential biological function of capsaicin in human gastric cancer cell line AGS.Total RNA was collected from AGS cells treated with capsaicin (at a dose of 250uM for 24h) or DMSO using TRIzol reagent according to the manufacturer’s protocol (n=3 per group). RNA was quantified using a NanoDrop ND-2000 (Thermo Scientific, USA), and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, USA). High throughput sequencing was performed by TsingKe biotech Co., Ltd. according to the manufacturers` standard protocols. The quality control and preliminary analysis of sequencing raw data was performed by Novogene biotech Co., Ltd. according to the standard pipeline. Gene expression level was measured by Fragments Per Kilobase of exon model per Million mapped fragments (FPKM).

INSTRUMENT(S): Agilent Bioanalyzer 2100 (Agilent Technologies, USA)., Illumina HiScanSQ, Not Appliciable, Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

ORGANISM(S): Homo sapiens

SUBMITTER: Jie Shen

PROVIDER: E-MTAB-14511 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic profile of valvular endothelial cells in normal and high glucose conditions, interacted with human monocytes (THP-1)

Project description:Human valvular endothelial cells were co-cultured with THP-1 monocytes in high glucose (33mM) or normal glucose (5mM) levels for 2 hours. Afterwards cells were lysed and total cellular RNA was extracted using TRIzol reagent.

2024-05-31 | E-MTAB-13766 | biostudies-arrayexpress

Shouchella clausii strain:ZBJDR1

Project description:Zytex Biotech Pvt. Ltd. Genome sequencing

| PRJNA1186385 | ENA

Defining Immune Heterogeneity in HNSCC with RNAseq

Project description:We collected up to 6 separate analytes per patient from 14 HNSCC individuals and evaluated spatial (9 cases) and/or temporal (8 cases) variability using RNAseq. Sections taken from a frozen section using a crytostat were analysed for RNA quality was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies UK Ltd., Stockport, UK). Total RNA was converted into a library for sequencing on the HiSeq 2000 (Illumina Inc., San Diego, USA) using the TruSeqâ¢ stranded mRNA Sample Preparation Kit (Illumina Inc.). Briefly, poly-A mRNA was purified from total RNA (100ng) using the Poly(A) Purist Mag Kit (Life Technologies Ltd., Paisley, UK), according to the manufacturerâs instructions. The mRNA was then amplified and converted into cDNA, which was purified and used to construct libraries that were hybridized to the flow cell for single end (SE 35bp) sequencing. The protocol employed yielded 35-bp long reads. The quality of raw SE read data in FASTQ files were assessed and reads of low quality were trimmed or removed. SE reads were then mapped to the human genome (hg19) using TopHat (version 2.0.9) and, following the removal of multi-mapping reads, converted to gene specific read counts for annotated genes using HTSeq-count (version 0.5.4).

2017-09-15 | E-MTAB-4546 | biostudies-arrayexpress

RNA-seq of Subcutaneous, Omental, and Retroperitoneal Adipose Tissues in a Cohort of Healthy Human Kidney Donors

Project description:This experiment aims to deepen our understanding of adipose tissue biology and its implications for metabolic and kidney health. The experimental workflow includes biopsy collection during surgery and total RNA extraction from each sample. Then cDNA libraries were prepared and used for high-throughput RNA sequencing.

2024-11-01 | E-MTAB-13869 | biostudies-arrayexpress

Transcriptional profiling of human Th9 T cell clones treated with GW9662 against untreated control

Project description:To investigate the role of PPAR-γ in human TH cells, transcriptional response of activated “TH9” clones to treatment with GW9662, a potent PPAR-γ antagonist was assessed. “TH9” cell clones were incubated with GW9662 for 48h and activated with αCD3/2/28 for 12 h. Transcriptomic profiling was performed by bulk RNA-seq. To generate TH9 clones, Peripheral Blood Mononuclear Cells (PBMC) were isolated by Ficoll-Plaque Plus (GE Healthcare, UK) density gradient centrifugation. Human CD4+ T cells were isolated from PBMC by EasySep positive selection kit (Stemcell Technologies) according to manufacturer’s instruction. Positively selected CD4+ T cells were washed with PBS and stained for subsequent TH cell subset sorting. Effector memory “TH9” cells (CXCR3-CCR8+CCR6-CCR4+) were sorted to over 90% purity according to their expression of chemokine receptors from CD45RA-CD25-CD8-CD3+ cells. Single cell “TH9” clones were directly sorted into 96well plate according to their expression of chemokine receptors (see above). Single cell clones were expanded and maintained by periodic restimulation with PHA (1 µg/ml, Sigma-Chemicals) and irradiated allogenic feeder cells (5x104/well) in culture medium.

2022-10-31 | E-MTAB-12197 | biostudies-arrayexpress

Transcriptional profiling of Th1, Th2, Th9, and Th17 T cell clones

Project description:We next sought to identify the transcriptional program that differentiates IL-9+Th2 cells from “conventional” Th2 cells. To this end, we selected representative Th1, Th17, Th2, and IL-9+Th2 clones (Figure 5A) and determined their transcriptome in the resting state and at different time points after activation using RNAseq. Peripheral Blood Mononuclear Cells (PBMC) were isolated by Ficoll-Plaque Plus (GE Healthcare, UK) density gradient centrifugation. Human CD4+ T cells were isolated from PBMC by EasySep positive selection kit (Stemcell Technologies) according to manufacturer’s instruction. Positively selected CD4+ T cells were washed with PBS and stained for subsequent Th cell subset sorting. Memory Th cell subsets were sorted to over 90% purity according to their expression of chemokine receptors from CD45RA-CD25-CD8-CD3+ cells: Th1(CXCR3+CCR8-CCR6-CCR4-), Th2 (CXCR3-CCR8-CCR6-CCR4+), Th17 (CXCR3-CCR8-CCR6+CCR4+), Th9 (CXCR3-CCR8+CCR6-CCR4+). Single cell Th subset clones were directly sorted into 96well plate according to their expression of chemokine receptors (see above). Single cell clones were expanded and maintained by periodic restimulation with PHA (phytohaemaglutinine, 1 µg/ml, Sigma-Chemicals) and irradiated allogenic feeder cells (5x104/well) in culture medium. T cells were polyclonally activated using beads coated with antibodies against CD3, CD2, and CD28 (T cell/bead = 2:1, human T cell activation/expansion Kit, Miltenyi). Cell cultures were sampled before activation (time 0h) and 2, 4, 6, 9, 12, 24, and 48 hours after activation.

2017-11-10 | E-MTAB-5739 | biostudies-arrayexpress

RNA-seq of Arabidopsis 14 day-old seedlings expressing either mCherry-RAX1-GR or mCherry-GR with 4h mock vs. dexamethasone treatment

Project description:In order to identify relevant target genes of RAX1 (AT5G23000) involved in meristem initiation in Arabidopsis we generated dexamethasone inducible lines expressing either a mCherry-RAX1-GR or a mCherry-GR (mock construct) fusion protein. We analysed differential gene regulation after 4 hours of dexamethasone or mock treatment in 14 day-old seedlings. Paired-end sequencing was performed using 3 biological replicate for each genotype and differentially expressed genes were identified for the interaction of genotype and treatment.

2019-07-01 | E-MTAB-7050 | biostudies-arrayexpress

RNA-seq of human primary epithelial nasal cells infected with SARS-CoV-2 (20A clade) and treated with long chain inorganic polyphosphates (polyP120) against vehicle-(saline solution)- treated controls

Project description:Primary human nasal epithelial cells collected by nasal brushing of healthy donors (data deposited at: EVA- EMBL-EBI; project ID: PRJEB42411; analyses: ERZ1700617) were plated (3x105 cells) and infected with SARS-CoV-2 viral particles 20A (EPI_ISL_514432-S66; MOI, 0.03). After 24 hours, the infected cells were treated with 18.5 microMolar long chain inorganic polyphosphates (polyP120) or vehicle (saline solution) as the negative control for the treatment. After 36 hours, the cells were lysed, and their RNA were extracted for RNAseq.

2024-05-31 | E-MTAB-13363 | biostudies-arrayexpress

RNA-seq of human uninfected Caco-2 cells treated with a nutraceutical formula (Solution-3), or vehicle-(saline solution)- control

Project description:Caco-2 cells were plated (1000000 cells) and treated with a nutraceutical formula (Solution-3) at 0.01x concentration or with vehicle (saline solution) as the negative control for the treatment. After 24 hours, the cells were lysed, and their RNA was extracted for RNAseq.

2024-06-20 | E-MTAB-14178 | biostudies-arrayexpress

RNA-seq of human HEK-293T cells treated with a nutraceutical formula (solution-3), or vehicle-(saline solution)-treated controls

Project description:HEK-293T cells were plated (1x106 cells) and treated with a nutraceutical formula (solution-3) at 0.01x concentration or with vehicle (saline solution) as the negative control for the treatment. After 24 hours, the cells were lysed, and their RNA was extracted for RNAseq.

2024-06-19 | E-MTAB-13918 | biostudies-arrayexpress

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