15020 results for "cancer studies using rna-seq"

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• Reference epigenome SMC01 mRNA-Seq data generated from KEP study

  SMC01 mRNA-Seq paired end data

  Dataset EGAD00001007169

• Reference epigenome SMC03 mRNA-Seq data generated from KEP study

  SMC03 mRNA-Seq paired end data

  Dataset EGAD00001007171

• Reference epigenome SMC04 mRNA-Seq data generated from KEP study

  SMC04 mRNA-Seq paired end data

  Dataset EGAD00001007172

• Reference epigenome ADMSC01 mRNA-Seq data generated from KEP study

  ADMSC01 mRNA-Seq paired end data

  Dataset EGAD00001007150

• Reference epigenome ADMSC03 mRNA-Seq data generated from KEP study

  ADMSC03 mRNA-Seq paired end data

  Dataset EGAD00001007152

• Reference epigenome IPS01_N_Fibroblast_smRNA-Seq data generated from KEP study

  A IPS01_N_Fibroblast_smRNA-Seq single end data for iPSC(Oct4)

  Dataset EGAD00001003501

• Reference epigenome IPS04_X_Fibroblast_mRNA-Seq data generated from KEP study

  A IPS04_X_Fibroblast_mRNA-Seq paired end data for iPSC(Oct4)

  Dataset EGAD00001003491

• Reference epigenome IPS01_N_Fibroblast_mRNA-Seq data generated from KEP study

  A IPS01_N_Fibroblast_mRNA-Seq paired end data for iPSC(Oct4)

  Dataset EGAD00001003488

• McGill EMC Release 4 for assay "ChIP-Seq Input"

  McGill EMC Release 4 for assay "ChIP-Seq Input"

  Dataset EGAD00001001293

• Reference epigenome IPS04_X_Fibroblast_smRNA-Seq data generated from KEP study

  A IPS04_X_Fibroblast_smRNA-Seq single end data for iPSC(Oct4)

  Dataset EGAD00001003504

• ATAC-Seq datasets in human islets

  13 ATAC-Seq datasets of human pancreatic islets from 13 donors

  Dataset EGAD00001005201

• WES of pleomorphic lung cancer

  Pulmonary pleomorphic carcinoma (PPC) is an aggressive and highly heterogeneous non-small-cell lung carcinoma whose underlying biology is still poorly understood. Forty-two tumor areas including 39 primary tumors and 3 metastases from 20 PPC patients were microdissected and the histologically distinct components were subjected to whole exome sequencing (WES) separately. Twist Human Core Exome + RefSeq + Mito-Panel kit (Twist Bioscience) was used for the whole exome capturing according to manufacturer’s guidelines. Paired-end 100-bp reads were generated on the Illumina NovaSeq 6000. After the sequencing, reads were aligned against the reference human genome GRCh38 using Burrows-Wheeler Aligner (BWA, v0.7.12)

  Dataset EGAD50000000453

• TMD-AMKL targeted follow-up

  Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50 ). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

  Dataset EGAD00001000783

• Variant calling for LUNG-NSCLC2 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. This dataset contains whole exome sequencing data from tumor samples processed with the Vegan pipeline. In the absence of matching germline samples, variant calling is performed using two panel of normals (one for female and one for male). It includes SNP and CNV calling.

  Dataset EGAD50000002235

• Single-cell RNA-sequencing of a multi-region pleural mesothelioma case

  Single-cell RNA-sequencing from three distant regions of an epithelioid pleural mesothelioma case.

  Study EGAS00001008062

• Whole Genome Profiling to Detect Schizophrenia Methylation Markers

  Schizophrenia (SCZ) is a devastating psychiatric disorder. The aim of this study was to detect DNA methylation (5meC) profiles in whole blood associated with SCZ. The sample consisted of schizophrenia cases and controls selected from national population registers in Sweden. We employed MBD protein-based enrichment of the methylated DNA fraction, followed by single end sequencing (50 bp reads) on the SOLiD platform. To improve methylome-wide coverage we used an existing protocol variant, which increases the relative number of fragments from CpG poor regions. To analyze the data, we used an analysis pipeline described elsewhere7, that was designed specifically for MBD-seq and included alignment, quality control (QC) of reads and samples, coverage calculations for the 26,752,702 autosomal CpGs in the reference genome using a non-parametric estimate of the fragment size distribution, an in silico experiment to identify CpGs in loci with alignment problems, a 2-stage adaptive algorithm to combine data from correlated adjacent CpG sites in "blocks", principal component analysis (PCA), association testing, bioinformatics annotation and network analysis. After QC, 1459 subjects with on average 32.4 million high quality reads remained. Association testing was performed on 4.3 million high quality blocks after regressing out possible assay related technical artifacts, sex/age, and unmeasured confounders through the PCA components.

  Study phs000608