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.
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
Project description:Insight on the understanding of the effect of maternal diabetes on embryonic nervous system development in embryos without neural tube defects. Control Group: Each sample (n) contained the RNA obtained by TRIZOL of a bulk of 30 prosencephalons (embryo day 12) of embryos from both sexes obtained from pregnant rats that were intraperitoneally injected with citrate buffer. n=3 Experimental group: Each sample (n) contained the RNA obtained by TRIZOL of A bulk of 30 prosencephalons (embryo day 12) of embryos from both sexes obtained from pregnant rats that were diabetic induced with an intraperitoneal administration of 50 mg/kg of streptozotocin. n=3 The sequence liberties were obtained through paired-end sequencing experiments. Codes for the files are as follows: Control E12: AM1_S1_R1_001.fastq.gz AM1_S1_R2_001.fastq.gz AM2_S2_R1_001.fastq.gz AM2_S2_R2_001.fastq.gz AM3_S3_R1_001.fastq.gz AM3_S3_R2_001.fastq.gz Diabetic E12: AM4_S4_R1_001.fastq.gz AM4_S4_R2_001.fastq.gz AM5_S5_R1_001.fastq.gz AM5_S5_R2_001.fastq.gz AM6_S6_R1_001.fastq.gz AM6_S6_R2_001.fastq.gz Were S = sample, R1 = sense sequencing, and R2 = antisense sequencing. Sequencing was performed on a NextSeq500 using the TruSeq HT kit from Illumina.
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.
Project description:Variation in transciptomic patterns between shallow and mesophotic corals was assessed using tag-based RNA-Seq (Tag-Seq) through analysis of natural populations across four regions in the Gulf of Mexico. Additionally, colonies were fate-tracked and repeatedly sampled to assess changes in gene expression through time in a transplant experiment between shallow and mesophotic depth zones at West and East Flower Garden Banks. This repository contains the raw .fastq.gz files for all sequenced samples.
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.