316466e5-1488-44e3-bad0-9f98f0854d68 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009265 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This dataset comprise results of mutect2 variant calling in vcf format on 9 samples of rosette forming brain tumors (5 with paired normal tissue and 4 without). Only variants specific to the tumor where kept to comply with patients consent.
| EGAD00001009266 | EGA
Project description:This GEO submission includes RNAseq raw data (fastq.gz) and processed data (using DESeq2) from samples obtained in the wild type and the pfd4 and 6x_pfd mutants
2020-12-22 | GSE138432 | GEO
Project description:Rosette-forming marine heterotroph
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Project description:Glioma study (gene expression and CGH): Brain tumours are the most common solid tumors in children and have the highest mortality rate of all solid pediatric tumours. Despite advances in multimodality therapy, children with high-grade gliomas invariably have an Overall Survival (OS) around 20% at 5 years. There is growing evidence that the biological knowledge and the histo-prognostic classifications used for the management of adult HGG may not fully apply to children. Interobserver variability and specificity of pediatric tumors with respect to the World Health Organization (WHO) classification have lead to a high rate of misclassification in multi-institutional studies. From 90 biopsies of children with HGG (High Grade Glioma), comprising 37 DIPG (Diffuse Infiltrating Pontine Glioma), 73 extracted RNA have been hybrized on Agilent 4x44K GE arrays and 71 extracted DNA have been hybrized on Agilent 44K and 4x44K CGH arrays. The dataset contains raw data files from Feature Extraction. Genomic data were jointly analysed with clinical and histological data comprising: date_of_diagnosis, date_of_last_news, WHO_grade, deceased_at_median_survival_time, deceased_at_2years, localization of the tumour in brain, gadolinium_T1_inf_T2. A specific analysis was performed on DIPG.
2012-02-22 | E-TABM-1107 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) technology was used to map expression profiles of effector (spleen) and key target tissues (kidney and brain) in mouse model of Systemic Lupus Erythematosus (SLE). Methods: Total RNA was extracted from total brain, total kidney and total spleen using Trizol and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Paired-end 37-bp mRNA sequencing was performed on Illumina HiSeq2000 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package. Results: We defined kidney-specific molecular signatures of the murine lupus transcriptome that mirrors nephritis-specific transcriptome alterations in human SLE. Conclusions: By the use of the mouse kidney-specific transcriptome and through training of a large whole-blood RNA-sequencing dataset of SLE patients, we developed and validated an algorithm that predicts patients with active LN from SLE patients without LN and suggest vigilance in the monitoring of these patients and potential enrollment in LN prevention studies.
2022-10-01 | GSE186367 | GEO
Project description:We have performed bulk RNA sequencing on colorectal tumors in order to determine their transcriptome-based molecular subtypes. RNA was isolated from fresh frozen human colorectal tumor specimens with Trizol extraction. RNA library preparation was performed with KAPA stranded mRNA sequencing kit, during which mRNA selection was performed with polyT capture beads. Sequencing was performed on Illumina HiSeq4000 as single-end 51 bp reads. File names include dataset name (KUL3), patient code(SCXXX), sample region (core or border) and sample code (EXTXXX): DATASETNAME_PATIENTCODE_SAMPLEREGION_rSAMPLE_CODE_...fastq.gz
2020-04-05 | E-MTAB-8412 | biostudies-arrayexpress
Project description:Introduction: Ependymoma (EPN) studies have revealed certain genetic markers, such as gain of chromosome 1q (1q+), as indicators of poor survival and high rate of recurrence. Development of novel therapeutics for EPN has been hampered by a lack of in vivo and in vivo models. We describe two unique 1q+ cell lines (811 and 928) derived from two children with metastatic, recurrent EPN. Both cell lines were characterized using histological, karyotypic and transcriptomic methods Transcriptomic analysis revealed that both lines, when cultured in 3D format, clustered closer to primary EPN tumors than monolayer format and with better fidelity of EPN-specific transcripts, namely those related to cilia function. Additionally, 3D culture histology revealed striking ependymal rosette formation, similar to primary tumors. Transcriptional enrichment of extracellular matrix, however, was a common signature of EPN primary tumor and cell lines in both monolayer and 3D formats.
2016-09-09 | GSE86574 | GEO
Project description:To exlore more circRNAs involved in Arabidopsis thaliana, we deeply sequenced 14 samples including whole plants from four developmental stages (rosette leaves > 1 mm in length; rosette growth complete; 50% of flowers to be produced have opened; first silique shattered), aerial part of plants from four stress treatments (control, drought, salinity and heat), five organs (roots, stems, leaves, flowers and siliques) and a mixed sample from whole plants across the lifespan (cotyledons emergence, rosette leaves﹥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and paired-end (PE) sequenced by Illumina HiSeq 2500 (read length, PE125, the mixed sample) and Illumina Hiseq X Ten (read length, PE150, 13 independent samples) platforms. We obtained 181.97 Gb raw data (151.37 Gb from 13 samples and 30.6 Gb from a mixed sample) and identified 5861 circRNAs with expression quantity. We annotated the parent genes of these circRNAs and predicted their target sites of microRNAs.
2016-09-01 | GSE77672 | GEO
Project description:This submission includes the complete set of raw data generated from the analytical standard, the concept of which is described in our manuscript "Proteome-Scale Recombinant Standards And A Robust High-Speed Search Engine To Advance Cross-Linking MS-Based Interactomics". In this study, we develop a strategy to generate a well-controlled XL-MS standard by systematically mixing and cross-linking recombinant proteins. The standard can be split into independent datasets, each of which has the MS2-level complexity of a typical proteome-wide XL-MS experiment. This submission includes 5 raw datasets (batches 1-5), each comprising 64 randomly selected human proteins engaging in up to 224 allowed protein-protein interactions per dataset. The data were searched with Scout (v. 1.4.14, https://github.com/diogobor/Scout) and results are reported in mzIdentML 1.2.0 format. For the specific results reported in our original publication, please refer to PXD042173.
2024-08-06 | PXD042173 | Pride