C7b48d06-6877-45d1-941a-593fef272a6b - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006656 | EGA |
REPOSITORIES: EGA
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Project description:For this project about non-muscle invasive bladder cancer (NMIBC), we analysed total RNA-seq data from 47 patients used for validation. Sequencing of total RNA was performed using KAPA RNA HyperPrep Kit with RiboErase HMR (Roche). RNA input was 100 to 500 ng. The dataset is composed of 94 fastq files.
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Project description:We retrospectively identified cases of invasive vulvar squamous cell carcinoma. Formalin fixed, paraffin embedded tissues samples were retrieved. Sections were confirmed by H&E staining prior to analysis. Sections were processed by ribosomal RNA depletion and RNA-sequencing (KAPA RNA HyperPrep with RiboErase) (HMR). 23 patient samples had RNA of sufficient quality for analysis. HPV status was determined by a consensus of high-risk HPV RNA-ISH and HPV DNA PCR. Only samples that were positive in both assays were considered 'HPV-positive'.
2022-01-01 | GSE183454 | GEO
Project description:Sample libraries were prepped using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned against the human genome (hg19) using STAR v2.5.4b2.
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Project description:Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect. 18 of 36 participants developed a replicative SARS-CoV-2 infection as evidenced by consecutive PCR-positive swabs for the virus. For every participant, blood RNA from selected days were extracted and depleted for genomic DNA and globin mRNA, before cDNA libraries were constructed using KAPA RNA HyperPrep with RiboErase kits. Libraries were sequenced on the Illumina NovaSeq 6000 platform using NovaSeq 6000 S4 Reagent Kits (200 cycles). Nose swab RNA samples were extracted and depleted for genomic DNA before cDNA libraries were constructed using KAPA mRNA HyperPrep Kits. Libraries were sequenced on the Illumina NextSeq platform the using the NextSeq 500/550 High Output Kit (75 cycles).
2024-04-08 | E-MTAB-12993 | biostudies-arrayexpress
Project description:RNA-seq was generated to investigate differences in gene expression between t(3;8) AML and other primary AMLs. Briefly, sample libraries were prepared using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina
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Project description:Purpose: With the advent of human genome sequencing project, circRNAs attracted widespread attention in cancer research due to its stable ring structure. Our aim was to identify differentially expressed circRNAs in GC and explore their potential roles in GC diagnosis and treatment. Methods: Total RNA from tissues was isolated by Hipure Total RNA Mini Kit (Magen, Germany). Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, California) was used for RNA concentration measurement while Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA) for RNA integrity estimation. A RIN value over 7.0 was considered eligible. RNA-seq library was prepared with approximately 2μg of total RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina® (Kapa Biosystems, Inc., Woburn, MA). Briefly, total RNA was incubated at 37 °C for 30 min with 10 units RNase R (Epicentre Technologies, Madison, USA) after removing ribosomal RNA. Next, the ribominus RNase R (+) RNAs was fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. Each library was diluted to 10 nM and pooled equimolar prior to clustering. Paired-End (PE150) sequencing was performed on all samples. Results: A total of 25,303 circRNA targets, including 20,036 known circRNAs and 5,267 uncharacterized circRNAs, were detected and defined. Among them, there were 2,007 circRNAs with statistically significant differences in expression in GC tissues, in which fold changes>2.0 and P<0.05 were identified.
2019-06-16 | GSE131414 | GEO
Project description:To identify the expression profiles of circRNAs in peripheral blood mononuclear cells (PBMCs) from Ankylosing Spondylitis (AS) patients and healthy controls, we used circRNA sequencing to detect circRNA in 3 samples of PBMCs from AS patients and 3 samples of PBMCs from healthy controls. In brief, total RNA was extracted and purified using Magen Hipure Total RNA Mini Kit (Magen, Guangzhou, China), followed by constructing RNA sequencing libraries with KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Inc., MA, USA). After the construction of RNA sequencing libraries, Qubit 3.0 fluorometer (Invitrogen, CA, USA) and the Agilent 2100 bioanalyzer (Applied Biosystems, CA, USA) were used for quality control. Then, the PE150 mode of HiSeq X10 (Illumina Inc., CA, USA) was used for sequencing. Differentially expressed circRNAs were screened with criteria of fold-change>1.5 and p<0.05.
2022-01-05 | GSE178408 | GEO
Project description:Our aim is to explore the effect of Hydroxy-carboxylic Acid Receptor 1 on cardiomyocytes. Neonatal rat cardiomyocytes (NRCMs) were isolated and cultured. Subsequently, NRCMs were treated with the agonist of Hydroxy-carboxylic Acid Receptor 1 (HCAR1), 3Cl-HBA at 40 μM for 48 h(HBA1,HBA2 and HBA3) or DMSO as control(C1,C3 and C3). RNA was extracted using the KAPA RiboErase RNA-Seq kit (Roche, Basel, Switzerland), and was analysed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) for quality control. The libraries were sequenced on an Illumina HiSeq X Ten platform. DESeq2 was used to analyse RNA-seq data. Neonatal rat cardiomyocytes (NRCMs) were isolated and cultured. Subsequently, NRCMs were treated with the agonist of Hydroxy-carboxylic Acid Receptor 1 (HCAR1), 3Cl-HBA (40 μM for 48 h) or DMSO as control. RNA was extracted using the KAPA RiboErase RNA-Seq kit (Roche, Basel, Switzerland), and was analysed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) for quality control. The libraries were sequenced on an Illumina HiSeq X Ten platform.
2024-02-14 | GSE224822 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived NGF-overexpressed LNCaP cells transcriptome profiling (RNA-seq) to microarray methods and to evaluate NGF signature for optimal high-throughput data analysis. Method: LNCaP/EV and LNCaP/NGF cells were cultured in RPMI 1640 medium supplemented with 10% FBS. An RNeasy Midi Kit (Qiagen, Redwood City, CA, USA) was used for total RNA isolation. The cDNA library was prepared by KAPA mRNA HyperPrep Kits (Roche) and sequenced using the NovaSeqTM 6000 sequencing system (Illumina, San Diego, CA, USA) in 300~400-bp paired-end reads. Results: Here we show that an androgen-deprivation therapy (ADT)-stimulated transcription factor, ZBTB46, upregulated NGF via ZBTB46 mediated-transcriptional activation of NGF. Our results reveal a role of the NGF in the development of NEPC that is linked to ZBTB46 upregulation. Conclusion: Our study provides evidence that the ZBTB46-NGF axis has potential to be considered as a therapeutic target to impair NEPC progression.
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