3743 results for "RNA AND sequencing OR transcriptome"

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• BE-scRNA

  This dataset contains single cell RNA-sequencing of BE samples by 10x Genomics. Total number of files - 28. File format - FASTQ.

  Dataset EGAD50000000753

• scRNA-seq Next GEM Single Cell 3ʹ

  Single-cell RNA sequencing (scRNA-seq) was generated using the 10x Genomics Chromium Next GEM Single Cell 3ʹ platform

  Dataset EGAD50000001185

• Pharmacogenomics of T-ALL

  Whole exome seq (N=21) and RNA-seq (N=36) data of additional T-ALL

  Dataset EGAD00001006434

• Single Nuclei RNA sequencing batch 2

  This dataset includes the 2 extra normal samples adjacent to PTC tumors that were multiplexed and profiled using kits from different batches.

  Dataset EGAD00001011364

• Comparison clinical recommendation MASTER and panel sequencing: RNA data

  This dataset contains 19 case/control samples of RNA sequencing data. Sequencing was performed on Illumina HiSeq 4000 and NovaSeq 6000 using TruSeq Stranded mRNA Kit. The sequencing was always paired.

  Dataset EGAD50000000625

• Sequencing data from the study "Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer"

  This dataset consists of 71 whole-genome samples and 47 RNA-seq samples. All WGS samples are provided in .bam format and RNA-seq samples are provided as .fq.gz (paired-end). Next-generation sequencing data on whole genomes were processed by aligning sequencing reads to a reference genome (NCBI build 37/hg19) using bwa-mem (0.7.13-r1126).

  Dataset EGAD50000001978

• Natural variation of circulating RNAs in human serum

  The Janus Serum Bank (JSB) is a population-based cancer research biobank. This dataset contains small RNA sequencing (RNA-seq) data of 520 JSB samples from cancer-free individuals. Sequencing libraries were indexed and 12 samples were sequenced per lane on a HiSeq 2500 (Illumina) to an average depth of 18 million reads per sample. The dataset files are raw FASTQ files from the sequencing machine (50bp, single-end sequencing)

  Dataset EGAD00001003968

• RNA-sequencing and targeted DNA-sequecing of human thyroid tumors and normal samples

  RNA-sequencing data: 5 normal thyroid tissues, 14 papillary thyroid carcinomas, 2 lymph node metastases, 19 poorly differentiated thyroid carcinomas and 17 anaplastic thyroid carcinomas; Targeted DNA-sequencing of the 165 genes included in the “Solid and Haematological tumors” panel (BRIGHTCore, Brussels, Belgium): 2 normal thyroid tissues, 2 poorly differentiated thyroid carcinomas and 7 anaplastic thyroid carcinomas; 2 FASTQ files for each sample (paired).

  Dataset EGAD00001011678

• Brain transcriptome of hereditary cerebral haemorrhage with amyloidosis–Dutch type (HCHWA-D)

  HCHWA-D is an early onset hereditary form of Cerebral Amyloid Angiopathy (CAA) caused by a point mutation resulting in an amino acid change (NP_000475.1:p.Glu693Gln) in the Amyloid Precursor Protein (APP). Post-mortem brain tissue (9 patients and 9 age-related controls; frontal and occipital cortex) was used for next generation sequencing of RNA (RNA-Seq with ribosomal RNA depletion).

  Study EGAS00001002730

• Host pathogen interaction long read transcriptome

  Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular in transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are predicted to be benign using the reference transcript annotation. In further support of SUsPECT’s utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.

  Study EGAS00001006779