12312 results for "cancer rna-seq"

in 19.22 milliseconds.

• Single Cell ATAC-Seq on human cord-blood derived HSPC.

  Study EGAS00001004740

• Gene-Specific RNA Sequencing in PLCG2-Associated Immune Dysregulation with Cold Urticaria

  This study utilized gene-specific RNA-sequencing of PLCG2 to screen for disease causing in-frame exon-skipping transcripts of PLCG2 in a collection of 9 subjects with cold urticaria, 2 subjects with known PLCG2-associated antibody deficiency and immune dysregulation (PLAID)-causing deletions of PLCG2 (positive controls) and 3 healthy subjects (negative controls). Full length cDNA of PLCG2 was generated using gene specific reverse transcription of peripheral blood mononuclear cell RNA. The full length PLCG2 cDNA was used as the template to create Illumina sequencing libraries. To identify the underlying genetic basis for the exon-skipping transcripts, trio-based whole genome sequencing was performed for probands in whom in-frame exon-skipping transcripts of PLCG2 were identified.

  Study phs003807

• HipSci RNA sequencing for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNA sequencing on commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines.

  Study EGAS00001001727

• Single cell RNA sequencing of bone marrow mononuclear cells

  Bone marrow aspirates were obtained from patients with relapsed/refractory large B cell lymphoma (rrLBCL), mononuclear cells isolated by ficoll density-gradient centrifugation, and loaded onto a 10X Chromium for single cell RNA-sequencing using 5’ chemistry without prior cryopreservation. Healthy donor bone marrow mononuclear cells were obtained from healthy allogeneic stem cell transplant donors and analyzed following viable cryopreservation.

  Study EGAS00001006836

• Single-cell Kinnex sequencing of Alzheimer's disease isoform profile

  Alzheimer’s disease (AD) is the most common cause of dementia, yet its molecular causes remain incompletely understood. RNA diversity in part arising from dysregulated splicing may contribute to AD pathogenesis; however, the ability to interrogate the resulting full-length isoforms in single brain cells has been technologically limited. Here we report the use of PacBio Kinnex long-read sequencing combined with 10X Genomics single-cell preparations to identify both annotated and unannotated RNA isoforms. Eight AD and seven non-diseased post-mortem human brains yielded ~70,000 single nuclei showing diverse, differentially expressed, and switched transcripts in multiple genes. Cell-type-specific isoform expression and variants with intra-exonic junctions associated with reverse transcriptase-mediated somatic gene recombination were also detected. Novel isoforms, including CHI3L1 and SEPTIN4, were altered in AD. Kinnex sequencing of RNA isoforms from single nuclei detected vast isoform diversity amongst brain cell types, representing an under-explored element in AD and other brain disorders.

  Study EGAS50000001476

• Identification of gene mutations and fusion genes in patients with Sézary Syndrome

  Sezary syndrome (SS) is a leukemic form of cutaneous T-cell lymphoma (CTCL) with an aggressive clinical course. The goal of our study is to understand the genetic basis of the disease by looking for driver gene mutations and fusion genes in 15 erythrodermic patients with circulating Sezary cels, fourteen of them fulfilling the diagnostic criteria of SS. Peripheral blood samples were collected for each patient and CD4+ T-lymphocytes and Granulocytes were isolated. DNA and RNA was extracted for matched normal and tumor materials. Whole exome sequencing was performed on matched normal and tumor tissues of 12 patients and RNA sequencing was performed on 10 patients. For 7 of these patients, we have both exome as well as RNA sequencing data. In this study, we present a complex genomic landscape of Sezary syndrome with several point mutations, copy number variations and fusion events which could contribute to the pathogenesis of SS.

  Study EGAS00001001706

• DAC for TCR-seq analysis of human intestinal Trm cells

  Dac EGAC00001001219

• scBCR-seq data from human donors

  Dataset EGAD00001005057

• Analysis of T cells in follicular lymphoma

  This study aimed to identify new heterogeneities in human T cells of follicular lymphoma. To do so, we performed scRNA-seq of human lymph node and follicular lymphoma samples. We identified minor T cell subsets expanding in follicular lymphoma.

  Study EGAS50000000778

• ChIP seq samples

  Dataset contains 12 ChIP-Seq samples sequenced on the Illumina NextSeq500 sequencer. 3 samples are control samples (HcAct-Chip 1,HcAct-Chip 2,HcAct-Imput 2) 9 samples are case samples (HcAct2DG-Chip 1,HcAct2DG-Chip 2,HcAct2DG-Imput 1,JIAAct-Chip1,JIAAct-Chip2,JIAAct-Imput2,JIAAct2DG-Chip1,JIAAct2DG-Chip2,JIAAct2DG-Imput2)

  Dataset EGAD50000001188

• Whole Genome DNA Methylation MPI

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Catalog No. 30024), the EZ DNA Methylation-Gold Kit (Zymo, D5005) and DNA Clean & Concentrator-5 (Zymo, D4013), following the instruction manual Accel-NGS® Methyl-Seq DNA Library (Revision 160510). Paired-end libraries (2 × 150 bp) were sequenced on a NovaSeq 6000 instrument.

  Dataset EGAD50000001139

• Whole Genome DNA Methylation

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences 30024), the EZ DNA Methylation-Gold Kit (Zymo D5005), and DNA Clean & Concentrator-5 (Zymo D4013), following the instruction manual Accel-NGS Methyl-Seq DNA Library (Revision 160510). Paired-end (2 x 150 bp) libraries were sequenced on a DNBSEQ-T7 instrument (MGI) after library conversion.

  Dataset EGAD50000000766

• CRC cell line ATAC-seq

  ATAC-Seq data for C32, CACO2, CL11, HT29, SW403, SW480, SW948 MSS CRC cell lines, and HCEC-1CT normal colon cell line

  Dataset EGAD50000000296

• Genomic landscape of IG-MYC positive Burkitt lymphoma with precursor B-cell immunophenotype.

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing of a rare Burkitt lymphoma subtype with precursor B-cell immunophenotype. Analysis were performed in concordance with the guidelines of the ICGC.

  Study EGAS00001002968

• BLUEPRINT September 2016, Bisulfite-Seq Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38

  Bisulfite-Seq data for 1 sample(s) Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38. 3 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001002969

• FASTQ files of the Exome-Seq data for the study "Genomic landscape of lung adenocarcinoma in East Asians"

  FASTQ files of the Exome-Seq data for both the normal and tumor samples for the study "Genomic landscape of lung adenocarcinoma in East Asians". For mutations and copy number variants called by this study, please download from https://src.gisapps.org/OncoSG_public/study/summary?id=GIS031 by clicking the download icon next to the dataset title.

  Dataset EGAD00001004422

• Mutational_burden_in_oesophagus__nanoseq_

  We wish to accurately assess mutational burden and signature from patients of different ages using clonal oesophageal epithelium and duplex-seq. We will also attempt to look for differences between smokers and non-smokers and individuals with different levels of alcohol consumption.

  Study EGAS00001007695

• BLUEPRINT release January 2015, Bisulfite-Seq for cytotoxic CD56-dim natural killer cell

  Bisulfite-Seq data for 3 cytotoxic CD56-dim natural killer cell sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001128

• BLUEPRINT release January 2015, Bisulfite-Seq for precursor lymphocyte of B lineage

  Bisulfite-Seq data for 1 precursor lymphocyte of B lineage sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001134

• BLUEPRINT release January 2015, Bisulfite-Seq for endothelial cell of umbilical vein (resting)

  Bisulfite-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001135

• BLUEPRINT release January 2015, ChIP-Seq for Acute promyelocytic leukemia

  ChIP-Seq data for 6 Acute promyelocytic leukemia sample(s). 25 run(s), 23 experiment(s), 23 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001138

• BLUEPRINT release January 2015, Bisulfite-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  Bisulfite-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001150

• BLUEPRINT release January 2015, Bisulfite-Seq for endothelial cell of umbilical vein (proliferating)

  Bisulfite-Seq data for 1 endothelial cell of umbilical vein (proliferating) sample(s). 21 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001151

• BLUEPRINT release January 2015, Bisulfite-Seq for CD4-positive, alpha-beta T cell

  Bisulfite-Seq data for 3 CD4-positive, alpha-beta T cell sample(s). 61 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001157

• BLUEPRINT release August 2015, Bisulfite-Seq for memory B cell, on genome GRCh38

  Bisulfite-Seq data for 1 memory B cell sample(s). 20 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001479