Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CircRNA in cervical cancer tissue

ABSTRACT: The sample library was built using ILUMIMA recommended kit, and the original data was sequenced using HiSeq 4000. The simple procedure is as follows: the sample RNA is reverse-transcribed into a cDNA, then a poly A is added at the 3’ End, then the sample is connected to the sequencing connector of the kit, and then PCR amplification is performed. Finally, HiSeq 4000 was used to detect the fault.

ORGANISM(S): Homo sapiens

PROVIDER: GSE169057 | GEO | 2021/03/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq from knee and hip osteoarthritis cartilage

Project description:In total, 70 samples on macroscopically preserved and lesioned OA cartilage from the same patient was taken for RNA-seq. Subsequently, paired-end 2×100 bp RNA library sequencing (Illumina TruSeq RNA Library Prep Kit, Illumina HiSeq 2000 and TruSeq Stranded Total RNA LT Sample Prep Kit, Illumina HiSeq 4000) was performed.

2019-01-07 | E-MTAB-7313 | biostudies-arrayexpress

Comparative transcriptome analysis of artificially induced rough-type Brucella strain RM57 and its parent strain

Project description:Purpose: To uncover the related mechanisms underlie virulence attenuation of RM57 vaccine candidate. Methods: Three Brucella melitensis M1981 strains and three Brucella melitensis RM57 strains were grown in TSB at 37℃ until the log phase was reached, total RNA was isolated using the TRIzol according to the manufacturer’s instructions.The sequencing library of each RNA sample was prepared by using NEB Next Ultra Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer.The HiSeq 4000 platform was used to perform the transcriptome sequencing. Results: The results revealed that expressions of 1205 genes were significantly different between RM57 and M1981. Data analysis showed that in the gene ontology term, the different expressed genes involved in energy production and conversion, and translation, ribosomal structure and biogenesis were significantly enriched. Pathway enrichment analysis indicated that the genes involved in oxidative phosphorylation, ribosome, nitrogen metabolism, tyrosine metabolism and two-component system were significantly affected.

2019-11-26 | GSE131394 | GEO

Single cell analysis of Monolayer and Organoid Primary Prostate Human Epithelial Cells Derived from the same patient

Project description:Single human primary prostate epithelial cells grown as a monolayer (2D) or as organoids (3D) were separated, collected and prepped for RNA-seq using the 10x Genomics Chromium Genome Reagent kit v2 Chemistry. 3,500-5,000 cells were collected from each sample and sequenced at a depth of ~45,000 genes per cells on a 2x150nt lane in a HiSeq 4000. CellRanger alignment was performed to produce the RAW data files.

2019-07-11 | GSE130318 | GEO

RNA-seq in mouse Th17 cells

Project description:Purpose: To gain more mechanistic insights into the effects of LDHB deletion on T cells, we performed RNAseq in WT and LDHB cKO Th17 cells which cultured in 5% O2. Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Approximately 60–80 million paired-end 150 bp reads were generated per sample using Illumina HiSeq 4000 platform Results: RNA-seq revealed quite small different transcriptome patterns

2023-03-29 | GSE190799 | GEO

Characterization of a Candida albicans Isolated from a recurrent Cervical Lymphadenitis Patient and it’s Clinic Indication

Project description:Purpose: To reveal the global regulatory genes of clinical strain, we performed comparative transcriptomic analyses of the SC5314 and JL01.Methods: We isolated a clinical Candida albicans strain JL01 (Jinling Hospital in Nanjing, China) from a 21-year-old man who presented to our hospital with recurrent cervical lymphadenitis. Cells of the JL01 and SC5314 were inoculated from overnight cultures by 1% into liquid YPD plus 10% serum medium at 37°C for 3 h. Cells were collected and total RNA was extracted as described. RNA-Seq analysis was performed by the company Majorbio (Shanghai, China). mRNA was purified, fragmented and used to synthesize cDNA. The library products were sequenced on the HiSeq 4000 platform using the HisSeq 4000 PE Cluster Kit and HisSeq 4000 SBS Kit.Results: 421 genes were significantly differentially regulated (P≤0.05, |log2FC|≥1) in JL01 compared with SC5314. Of these 421 DEGs (differentially expressed genes), 216 were up-regulated, and 205 were down-regulated. Conclusions: Together the clinical, morphological and biological analyses, we suggest that azole drug resistance, invasive defect and hypo-virulence of the JL01 strain may correlate with its contribution in chronic fungal infection.

2019-06-07 | GSE110291 | GEO

HiSeq 4000 / 10X Whole Genome Sequencing of Selected GeT-RM Coriell Samples with Consensus Calls for up to 28 Pharmacogenetics Genes

Project description:Polaris HiSeq 4000 PGx 10X Cohort

| PRJEB26950 | ENA

Prostaglandin E2 inhibits pro-fibrotic function of human pulmonary fibroblasts by disrupting Ca2+-signaling

Project description:Purpose: Identification of gene expression in human lung fibroblasts, including analysis of impact of IPF (Idiopathic Pulmonary Fibrosis) as well as TGFβ stimulation, with particular emphasis on prostanoid receptors and related pathways. Methods: Truseq stranded mRNA sequencing, via Illumina Hiseq 4000. Single reads, 75bp, ~25 million reads per sample. Quantification of gene expression in TPM using Kallisto, followed by Tximport. mRNA isolated via Qiagen RNeasy kit, with on-column DNase1 digestion. Results: Quantification of gene expression in primary human lung fibroblasts, including quantification of prostanoid GPCRs.

2019-03-01 | GSE119007 | GEO

Transcriptome of in vitro fertilized 7-day-old bovine blastocysts

Project description:Blastocysts consist of cells that form the inner cell mass and the trophectoderm. The full transcriptome of bovine blastocyst embryos was examined in this study. Total RNA was isolated from three independent batches of blastocysts. Using Poly(A) capture mRNA was isolated and cDNA libraries prepared using Illumina TruSeq RNA sample Prep Kit. The libraries were sequenced using Illumina HiSeq 4000. This dataset should serve as a baseline for understanding bovine pluripotency and trophoblast stem cells providing a snapshot for functional interpretation of preimplantation embryo development.

2021-10-17 | GSE169674 | GEO

RNA-seq in mouse WT and ABAT cKO T cells

Project description:Purpose: To gain more mechanistic insights into the effects of ABAT deletion on T cells, we performed RNAseq in activated CD4 WT and ABAT cKO TH0 cells. Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Approximately 60–80 million paired-end 150 bp reads were generated per sample using Illumina HiSeq 4000 platform Results: RNA-seq revealed an decreased pro-inflammatory gene signature in ABAT cKO T cells after activation Conclusions: Inhibition of ABAT suppresses TH17 but enhances iTreg cell differentiation

2022-08-02 | GSE190818 | GEO

RNA seq in CD8T cells

Project description:Purpose: we evaluated the T cell mediated anti tumor immune response under asparagine restriction Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Approximately 60–80 million paired-end 150 bp reads were generated per sample using Illumina HiSeq 4000 platform Results: We performed gene expression profiling analysis using data obtained from RNA-seq of T cells cultured in presence and absence of asparagine at 3 different time points and found that asparagine restriction induces biphasic response in T cell.

2023-06-15 | GSE201870 | 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