15000 results for "cancer studies using rna-seq"

in 34.65 milliseconds.

• MGUS/SMM to MM WES

  This dataset contains raw sequencing reads for matched MGUS/SMM to MM patient samples, including normal germline controls. FASTQ files were generated on Illumina NextSeq 500 and HiSeq 4000 machines following exome capture using the Agilent Clinical Research Exome kit. DNA was extracted from CD138+CD38++ cells (representing MGUS/SMM/MM cells) and CD138-CD38- (representing normal cells) isolated from bone marrow. 10 patients are included with 3 samples each representing normal, MGUS/SMM, MM stages.

  Dataset EGAD00001004190

• DNA Methylation-based diagnostic biomarkers for ESCC in Han Chinese population

  To validate the methylation status of the four candidate tumor suppressor genes (ADHFE1, EOMES, SALL1, TFPI2) in Han Chinese ESCC patients, we recruited 103 patients and obtained the paired tumors(entitled as T) and adjacent normal tissues (entitled as N) as well. Targeted bisulfite sequencing was conducted to detect the methylation profiles of these four genes in these 103 paired tissues. Furthermore, the raw sequence data (fastq files) was aligned using the BSseeker2 and this dataset included all of the bam file after alignment.

  Dataset EGAD00001004288

• Genomic profiling of Follicular thyroid adenomas and carcinomas using exome-sequencing analyses

  This dataset was conceived to characterize the genomic differences among different types of follicular-like thyroid lesions. To do so, we performed whole exome sequencing experiments on human biopsies corresponding to nodular hyperplasias, follicular thyroid adenomas, follicular thyroid carcinomas and Follicular Variant Thyroid Gland Papillary Carcinomas.

  Dataset EGAD00001008022

• Pseudotime ordering of cell cycle state (2020-01-29)

  We will be using G&T method to sequence single cell genome and transcriptome derived from FS13B iPSCs cell line. The cell cycle state of each of the single cells is known. Hence, we will be analysing the genome and transcriptome of single cells from each of the cell cycle state to generate a copy number profile and transcriptome profile per given cell cycle stage: G1, S, G2, S. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005919

• WGS data subfolder HFF7VCCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HFF7VCCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001007075

• The impact of the human leukaemia virus HTLV-1 on host gene expression

  PBMCs were purified from blood samples of 8 HTLV-1 infected individuals, and cryo-preserved in fetal calf serum containing 10% DMSO. DNA from each samples was extracted using Qiagen Blood & Tissue kit according to the manufacturer's protocol. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001004169

• Amplicon-based sequencing of drug resistant organoids

  A BRAF V600E colorectal organoid which is sensitive to MAP kinase inhibition was mutagenised with the chemical mutagen ENU and then drug selected using a combination of Trametinib, Dabrafenib and Cetuximab. Single cell derived organoids were then manually picked and expanded in drug. Resistance was confirmed in a 14 day assay and DNA was collected. These then underwent targeted amplicon-based sequencing to confirm candidate resistance effectors from a screen in 2 2D BRAF V600E colorectal cell lines. Pools of resistant clones were also sequenced.

  Dataset EGAD00001003248

• WCDT Hi-C assays performed mCRPC biopsies

  Paired FASTQ files from a Hi-C assay performed on mCRPC tumors. Sequencing was performed using 150nt paired reads generated by a Novaseq 6000 instrument.

  Dataset EGAD00001009408

• Deep WGS of matched tumor-normal pairs for HGSOC copy-number signatures study

  This dataset includes 111 bam files from WGS sequence data aligned to human genome assembly GRCh37 (hg19) from 56 tumour and matched normal samples. Libraries were constructed with ~350-bp insert length using the TruSeq Nano DNA Library prep kit (Illumina) and sequenced on an Illumina HiSeq X Ten System in paired-end 150-bp reads mode. The average depth was 60× (range 40-101×) in tumours and 40× (range 24-73×) in matched blood samples.

  Dataset EGAD00001004189

• Deep sequencing analysis of human iPSC-specific SNVs in donor cell population

  CR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001000605

• VCF file from 16 patients affected by acute intermittent porphyria

  VCF file from 16 patients affected by acute intermittent porphyria. Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). BAM files were processed at the CNAG (Barcelona) with their pipeline, including GATK v3.6 for genotyping and other tools such as snpEff for annotating variants, to produce this VCF file with a total of 10,630,259 variants, out of which 8,731,523 are SNVs.

  Dataset EGAD00001006952

• TGF-β signaling mediates microglial resilience to spatiotemporally restricted myelin degeneration

  Microglia survey and regulate central nervous system myelination during embryonic development and adult homeostasis. However, whether microglia-myelin interactions are spatiotemporally regulated remains unexplored. By examining spinal cord white matter tracts, we found that myelin degeneration was particularly prominent in the dorsal column (DC) during normal aging. This was accompanied by molecular and functional changes in DC microglia as well as an upregulation of TGF-β signaling. Disrupting TGF-β signaling in microglia led to unchecked microglial responses and myelin loss in the DC, accompanied by neurological deficits exacerbated with aging. snRNA-seq revealed the emergence of a TGF-β signaling-sensitive microglial subset and a disease-associated oligodendrocyte subset, both spatially restricted to the DC. We further discovered that microglia rely on a TGFβ autocrine mechanism to prevent damage of myelin in the DC. These findings demonstrate that TGF-β signaling is indispensable for maintaining microglial resilience to myelin degeneration in the DC during the aging process. This highlights a previously unresolved checkpoint mechanism of TGF-β signaling with regional specificity and spatially restricted microglia-oligodendrocyte interactions.

  Study EGAS50000001413

• Genes associated with pancreas development and function maintain open chromatin in iPSCs generated from human pancreatic beta cells

  Current in-vitro islet differentiation protocols suffer from heterogeneity and low efficiency. Induced-pluripotent stem cells (iPSCs) derived from pancreatic beta-cells (BiPSCs) preferentially differentiate towards endocrine pancreas-like cells versus those from fibroblasts (FiPSCs). We interrogated genome-wide open chromatin in BiPSCs and FiPSCs via ATAC-seq, and identified ~8.3k significant, differential open chromatin sites (DOCS) between the two iPSC subtypes (FDR<0.05). DOCS where chromatin was more accessible in BiPSCs (Bi-DOCS) were significantly enriched for known regulators of endodermal development, including bivalent and weak enhancers, and FOXA2 binding sites (FDR<0.05). Bi-DOCS were associated with genes related to pancreas development and beta-cell function, including transcription factors mutated in monogenic diabetes (PDX1, NKX2-2, HNF1A; FDR<0.05). Moreover, Bi-DOCS correlated with enhanced gene expression in BiPSC-derived definitive endoderm and pancreatic progenitor cells. Bi-DOCS therefore highlight genes and pathways governing islet-lineage commitment, which can be exploited for differentiation protocol optimisation, diabetes disease modelling, and therapeutic purposes.

  Study EGAS00001002591

• Multifocal_Breast_Project

  Comparison of genomic rearrangements and DNA methylationpatterns between different foci of multiple synchronous(multifocal and multicentric) invasive breast cancers

  Study EGAS00001000004

• COLO-829/COLO-829BL

  COLO-829 is a publicly available immortal cancer cell line and COLO-829BL is a lymphoblastoid cell line derived from the same patient

  Dataset EGAD00000000055

• scRNAseq data from metastatic breast cancer samples

  Paired-end SMARTseq2 data of EpCAM+ sorted cells from liquid biopsies from 3 patients. Sequencing was performed on Illumina HiSeq 2500.

  Dataset EGAD50000000816

• MD Anderson Cancer Center HGSOC LRS Data Access Comittee

  Oxford Nanopore long-read sequencing was performed on six paired tumor-normal samples from patients with high-grade serous ovarian carcinoma. Reads were mapped to the GRCh38 reference genome, incorporating base modification information.

  Dac EGAC50000000597

• DAC for lymphoma IFZ Essen

  This DAC is set in place to handle acess to data on lymphomas and immune cells submitted by scientists from the Institute of Cell Biology (Cancer Research) at the University of Duisburg-Essen in Essen, Germany.

  Dac EGAC50000000521

• Gastric Cancer Organoid Cultures and Tumors RNASeq Data

  RNASeq data generated from organoid cultures established from gastric cancers and normal mucosae, paired tumor frozen tissues, and cultured fibroblast.

  Dataset EGAD00001004302

• Illumina_WXS_MET-CELL-XEN

  Whole-exome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from PDO culture derived from colorectal cancer metastasis sample

  Dataset EGAD00001002097

• GEL WGS Comparison

  These samples are to be analysed with the CGP Developed cancer panel and the results will be compared with WGS data from 4 different comercial providers.

  Dataset EGAD00001000872

• Sequencing data for Murtaza et al. Nature Communications 2015 (doi:10.1038/ncomms9760)

  Exome and targeted amplicon sequencing data for tumor, germline and plasma samples from a patient with metastatic breast cancer.

  Dataset EGAD00001002108

• Illumina_WGS_T-XEN-CELL

  Whole-genome sequencing on Illumina HiSeq2000/2500 of PDO culture derived from Patient-derived xenograft derived from colorectal cancer primary tumor sample

  Dataset EGAD00001002092

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0150_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0150_002 for Triple negative breast cancer sample SA609X5XB03231

  Dataset EGAD00001011213

• Genome and transcriptome sequence data from a NUT midline carcinoma tumor patient

  Genome and transcriptome sequence data from a NUT midline carcinoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015289

• Genome and transcriptome sequence data from a minimally invasive adenocarcinoma tumor patient

  Genome and transcriptome sequence data from a minimally invasive adenocarcinoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015297

• Genome and transcriptome sequence data from a neurofibromatosis type 1 tumor patient

  Genome and transcriptome sequence data from a neurofibromatosis type 1 patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015301

• Illumina_RNA_T-CELL-XEN

  RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from PDO culture derived from colorectal cancer primary tumor sample

  Dataset EGAD00001002079

• Sequencing data for the manuscript "Multi-focal sampling of de novo metastatic prostate cancer reveals complex polyclonality and enables accurate clinical genotyping"

  This submission includes targeted and whole exome paired-end fastq files.

  Dataset EGAD00001009651

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0175_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0175_001 for Triple negative breast cancer patient-derived xenograft SA535X6XB03101

  Dataset EGAD00001011224

• Genome and transcriptome sequence data from a metastatic alveolar rhabdomyosarcoma tumor patient

  Genome and transcriptome sequence data from a metastatic alveolar rhabdomyosarcoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015295

• Illumina_WGS_MET-CELL-XEN

  Whole-genome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from PDO culture derived from colorectal cancer metastasis sample

  Dataset EGAD00001002086

• Genome and transcriptome sequence data from a acute lymphoblastic leukemia tumor patient

  Genome and transcriptome sequence data from a acute lymphoblastic leukemia patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015285

• scRNA mCRC PDO

  Chromium 10x scRNA of 6 metastatic colorectal cancer organoids

  Dataset EGAD00001008734

• Gastric Cancer Organoid Cultures and Tumors Whole Exome Sequencing Data

  Whole exome sequencing data generated from organoid cultures established from gastric cancers, paired gastric tumor frozen tissues and blood leukocyte DNA.

  Dataset EGAD00001004301

• Illumina_RNA_MET-CELL_Passages

  RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample at early/late passages

  Dataset EGAD00001002884

• Genome and transcriptome sequence data from a relapsed wilms tumor tumor patient

  Genome and transcriptome sequence data from a relapsed Wilms tumor patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015304

• Illumina_RNA_T-XEN-CELL

  RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from Patient-derived xenograft derived from colorectal cancer primary tumor sample

  Dataset EGAD00001002081

• Illumina_WGS_T-CELL-XEN

  Whole-genome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from PDO culture derived from colorectal cancer primary tumor sample

  Dataset EGAD00001002090

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0079_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0079_001 for Triple negative breast cancer sample SA1035X6XB03216

  Dataset EGAD00001011241

• Genome and transcriptome sequence data from a papillary thyroid carcinoma tumor patient

  Genome and transcriptome sequence data from a papillary thyroid carcinoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015303

• Nanopore low-pass WGS of human brain tumors

  Nanopore low-pass WGS of human brain tumors for evaluation of DNA methylation-based classification of cancer

  Dataset EGAD00001009663

• Genome and transcriptome sequence data from a malignant rhabdoid tumour tumor patient

  Genome and transcriptome sequence data from a malignant rhabdoid tumour patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015310

• Genome and transcriptome sequence data from a recurrence nasopharyngeal rhabdomyosarcoma tumor patient

  Genome and transcriptome sequence data from a recurrence nasopharyngeal rhabdomyosarcoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015314

• Genome and transcriptome sequence data from a pineal parenchymal tumor tumor patient

  Genome and transcriptome sequence data from a pineal parenchymal tumor patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015317

• Spatial Maps of Prostate Cancer Transcriptomes

  A total of 14 samples that has been analyzed with the Spatial Transcriptomics method. H&E stain can be sent if requested.

  Dataset EGAD00001004121

• Genome and transcriptome sequence data from a choroid plexus carcinoma tumor patient

  Genome and transcriptome sequence data from a choroid plexus carcinoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015321

• Genome and transcriptome sequence data from a malignant rhabdoid tumor tumor patient

  Genome and transcriptome sequence data from a malignant rhabdoid tumor patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015323

• Genome and transcriptome sequence data from a NUT midline carcinoma tumor patient

  Genome and transcriptome sequence data from a NUT midline carcinoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015325

• Genome and transcriptome sequence data from a acute myeloid leukemia tumor patient

  Genome and transcriptome sequence data from a acute myeloid leukemia patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015331