Ena-DATASET-WHG-15-05-2019-16:05:18:516-210 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005022 | EGA |
REPOSITORIES: EGA
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Project description:Here we describe CapTrap-Seq, an experimental workflow designed to address the problem of reduced transcript end detection by long-read RNA sequencing methods, especially at the 5' ends. We apply CapTrap-Seq to profile transcriptomes of the human heart and brain and we compared the obtained results with other library preparation approaches. CapTrap-Seq is a platform-agnostic method and here tested the method by using 3 different long-read sequencing platforms: MinION (ONT), Sequel (PacBaio) and Sequel II (PacBio).
2023-12-20 | E-MTAB-13063 | biostudies-arrayexpress
Project description:The LRGASP challenge encompasses different human, mouse, and manatee samples sequenced using multiple combinations of protocols and platforms. Different challenges will use distinct subsets of the samples for evaluation. The long-read sequencing platforms used in these challenges are the Pacific Biosciences (PacBio) Sequel II, Oxford Nanopore (ONT) MinION and PromethION. Samples will also be sequenced on the Illumina HiSeq 2500. The primary LRGASP library prep protocols are “standard” cDNA sequencing, direct RNA sequencing, R2C2, and CapTrap. Each sample will also include Lexogen SIRV-Set 4 spike-ins. We will also provide simulated PacBio and ONT data as part of the evaluations. This particular study focuses on single strand CAGE sequencing of human iPSCs, defining CAGE peaks from Illumina HiSeq 2500 (SR: 150 cycles) of two biological replicates for use in the LRGASP challenge.
2021-10-27 | GSE185917 | GEO
Project description:In this study, Genome-wide transcriptomes of CD8+ T cells from HCV/HIV co-infected or mono-infected treatment-naive individuals were analyzed by using microarray assays. Pairwise comparisons were performed and differentially expressed genes were identified followed by quantitative real time PCR (qRT-PCR) validation. To identify the important functional categories, Directed Acyclic Graphs (DAG) from Web-based Gene SeT AnaLysis Toolkit (WebGestalt) was used to find out Gene Ontology (GO) categories with significantly enriched gene numbers. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were also obtained by using the similar methods in the same website.
2012-05-17 | E-MEXP-3635 | biostudies-arrayexpress
Project description:RNA sequencing of Coxsackie virus by ONT MinION
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Project description:BackgroundWomen living with HIV (WLWH) are at higher risk of acquisition and progression of human papillomavirus (HPV) infection. Evidence on effect of HPV vaccination in this population is limited.MethodsThis phase IV randomized controlled observer-blind study assessed immunogenicity and safety of two HPV vaccines (AS04-HPV-16/18 vs. 4vHPV) given in WLWH (stage 1) and HIV- females aged 15-25 years. Co-primary endpoints were to demonstrate, in WLWH subjects, non-inferiority (and if demonstrated, superiority) of AS04-HPV-16/18 vs. 4vHPV for HPV-16 and HPV-18 by pseudovirion-based neutralization assay (PBNA) at month 7 and safety. Non-inferiority criteria was lower limit (LL) of the 95% confidence interval (CI) of the GMT ratio AS04-HPV-16/18/4vHPV above 0.5, in the according to protocol population. NCT01031069.FindingsAmong 873 subjects recruited between 26-Oct-2010 and 14-May-2015, 546 were randomized (1:1) and received at least one vaccine dose (total vaccinated cohort, TVC): 257 were WLWH (129 AS04-HPV-16/18; 128 4vHPV) and 289 were subjects without HIV (144 AS04-HPV-16/18; 145 4vHPV). Baseline CD4 cell count in WLWH was at least 350 cells/mm3.At month 7, AS04-HPV-16/18 showed immunological superiority to 4vHPV in WLWH. Neutralizing anti-HPV-16 and HPV-18 antibody GMTs were 2·74 (95% CI: 1·83; 4·11) and 7·44 (95% CI: 4·79; 11·54) fold higher in AS04-HPV-16/18 vs. 4vHPV (LL of the GMT ratio >1 in TVC, p<0·0001), respectively. Similar results were observed by ELISA up to month 24.Solicited local and general symptoms were in line with product labels. The number of reported serious adverse events (SAEs) was balanced throughout the study.InterpretationBoth vaccines showed an acceptable safety profile in all subjects. Despite the absence of an immunological correlate of protection for HPV, differences in immune responses elicited by the vaccines especially for HPV-18 may translate into longer lasting or more robust protection against cervical cancer with the AS04-HPV-16/18 vaccine in WLWH.
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Project description:The title compound, C(22)H(20)Cl(8)O(4), was prepared as part of the synthesis of precursors for the preparation of fluorinated mol-ecular tweezers. The mol-ecule sits on an inversion center, thus requiring that the cyclo-octane ring adopt a chair conformation.
| S-EPMC3007477 | biostudies-literature