16802 results for "sec+and+unspecified+malignant+neoplasm"

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• IBD WES trio data-ALPI-P2

  This project focused on identifying rare coding variation that substantially increases risk of VEOIBD by exome sequencing of VEOIBD patients and some of their family members. Here you can find BAM files from an affected proband (P2) and his unaffected parents. In this study ALPI mutations were identified as a likely cause of the disease.

  Dataset EGAD00001004485

• Single-cell RNA-seq of immune cells from Melanoma tumors (Li et al, 2018)

  Single-cell RNA-seq profiling of immune cells sorted from human Melanoma tumors (and several matching PBMC samples). Contains de-multiplexed FASTQ files per plate (MARS-seq amplification batch, total 204 samples) and also de-multiplexed FASTQ files of single-cell TCRb-seq.

  Dataset EGAD00001004497

• sQTL summary statistics

  This dataset contains the sQTL summary statistics (nominal pass, significant sQTLs). sQTL mapping was performed with QTLtools. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity.

  Dataset EGAD00001005042

• The transcriptome and DNA methylome profiling of the early human post-implantation embryos

  whole genome sequencing data of parent blood samples. Single cell full-length RNA-seq and PBAT-Seq data of in vitro culture D6 to D14 human embryo.

  Dataset EGAD00001005137

• Ribodepletion RNA-Seq of 8 samples and polyA RNA-Seq of 22 samples

  Ribodepletion RNA-Seq of 8 samples and polyA RNA-Seq of 22 samples

  Dataset EGAD00001004993

• WGBS analysis corresponding to representative cases of iBCP-ALL patients

  This dataset was conceived to characterize the epigenomic landscape of representative iBCP-ALL subtypes. To do so, we performed Whole Genome DNA bisulfite-sequencing on 2 MLL-AF4, 2 MLL-AF9 and 2 non-MLL rearranged leukemias, and also 2 pools of BCPs obtained from fetal liver.

  Dataset EGAD00001005010

• Whole-exome and whole-genome sequencing data

  Multi-omic data for lung neuroendocrine neoplasms, including the first multi-omic sequencing data for the understudied lung atypical carcinoids. The data includes Whole-exomes, whole-genomes, RNA-seq, and EPIC 850K methylation array data.

  Dataset EGAD00001005087

• Genomic profiling of patient-derived xenograft models of myxoid liposarcoma either sensitive or resistant to trabectedin

  The dataset consists of two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. Both models underwent the same treatment schedule with trabectedin (tree time points and one treatment with doxorubicin). We performed genomic profiling using Agilent OneSeq assay.

  Dataset EGAD00001005099

• EFFORT/LifeLines control human stool metagenomes (46 samples)

  Metagenomes of stool samples from 46 Lifelines control subjects (no antimicrobial use in the past three months before sampling, no occupational lifestock contact). Samples were sequenced and analysed as part of the EFFORT project and derived from the LifeLines cohort from the Northern parts of the Netherlands. http:///www.lifelines.nl.

  Dataset EGAD00001005443

• LBC1921 VCF

  LBC1921 and LBC1936 GVCFs called with GATK's HaplotypeCaller were combined and subject to variant quality score recalibration. This VCF contains the subset of samples (n = 296) from the LBC1921 cohort.

  Dataset EGAD00001005477

• Whole Exome Sequencing of 5 FFPE prostate samples (normal and tumour pairs) to identify mutations

  Whole Exome Sequencing was performed on radical prostatectomy formalin-fixed paraffin-embedded sample pairs (n = 6). Library prep was done by exon capture using the Illumina Truseq Exome kit and sequenced as 75bp paired end on Illumina NextSeq 500. Sequences were aligned to the human genome (hg38) using BWA.

  Dataset EGAD00001006107

• Survival Benefit and Genetic Profile of Pemetrexed as Initial Chemotherapy in Selected Chinese Patients with Advanced Lung Adenocarcinoma

  NGS data of 12 patients enrolled in the Chinese Patient Assistance Program from multiple centers who received pemetrexed alone or combined with platinum as initial chemotherapy and continued pemetrexed maintenance therapy for advanced lung adenocarcinoma from November 2014 to June 2017.

  Dataset EGAD00001006287

• Selected samples from the Boston Children's Hospital Childrens Rare Disease Cohorts initiative

  These are some selected exomes from the first year of the Childrens Rare Disease Cohorts initiative at Boston Children's Hospital. Patients were drawn from the following cohorts: immunodeficiency, epilepsy, IBD, hearing loss, and orphan diseases. Raw sequencing was performed on Illumina NovaSeq 6000 machines, and aligned to hs37d5.

  Dataset EGAD00001006179

• DNA repair knockouts

  We generated HPRT-only knockout lines as well as the combination of HPRT with MSH2, UNG and XPC. Whole genome sequencing was performed on generated clones and subclones. By subtracting variants present in the clones from those in the subclones, the somatic mutations, that accumulated in between the clonal steps, were determined.

  Dataset EGAD00001006777

• RNA-seq on neuroblastoma PDX model COG-N-519 treated with control miR-1283 and test miR-99b-5p mimics

  RNA-sequencing on neuroblastoma PDX model COG-N-519 treated with control miR-1283 and test miR-99b-5p mimics. Three samples from each of the treatment condition were analysed. Next-Seq platform was used for sequencing.

  Dataset EGAD00001007754

• Dataset-linking-WGS-via-README-for-EGAS00001004884

  This dataset contains 139 Tumor and Control WGS files for samples for Gerhauser et al.,Cancer Cell, 2018, 34:996-1011. WGS and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001007669

• sWGS of matched patient and PDX ovarian tumour tissues

  This dataset contains 8 .bam files of shallow WGS (~0.1×) from fresh frozen tumour tissues of four matched patients and first generation PDX models. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008650

• Novel method for efficient establishment, expansion and drug response profiling of high-grade serous ovarian cancer organoids

  HGSOC patient-derived organoids and their tissue of origin

  Dataset EGAD00001008753

• Pre-neoadjuvant treatment biopsy RNAseq breast cancer dataset

  This dataset contains RNAseq data of n=87 pre-treatment biopsies of triple negative and luminal- type breast cancer patients, all scheduled to receive neoadjuvant chemotherapy. Gene expression data is linked with treatment response and survival.

  Dataset EGAD00001008433

• Second primary vs. primary bowel malignancies

  Data about copy number aberrations was obtained from primary CRC (n=90). DNA was collected from second primary CRC (in HL survivors, n = 39), and primary SBA (n=14). For second primary SBA (in HL and TC survivors), DNA was isolated for molecular analyses (n=7). Copy number aberrations were evaluated after low-coverage whole genome sequencing.

  Dataset EGAD00001008476

• A life history of colorectal cancer metastases

  Multiple metastatic sites were sampled at autopsy from four patients diagnosed with metastatic colorectal cancer and subjected to whole-genome sequencing using the Illumina HiSeq X Ten platform to identify somatic variants, structural rearrangements and mutational signatures. The number of tumour samples per patient ranged from 6 to 66.

  Dataset EGAD00001007503

• Single cell study of infant leukemias

  We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.

  Dataset EGAD00001007853

• Human Hi-C

  This dataset contains 2 human tumor-derived cell lines and 1 human tumor Hi-C samples. The raw fastq files and the processed .hic file is provided for each sample.

  Dataset EGAD00001009050

• Sequence of breast cancer bone metastases PDX before and after palbociclib treatment resistance

  RNAseq sequencing of 10 breast cancer bone metastasis PDX. Samples were obtained from 5 PDX that acquired palbociclib resistance (palboR) and 5 from the parentale PDX (palboS).

  Dataset EGAD00001009068

• Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post- therapy medulloblastoma

  Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post- therapy medulloblastoma (2 samples). One sequencing was done on GridION, the other one on a P2 Solo. In both cases the SQK LSK-109 Kit was used for preparation.

  Dataset EGAD00001009490