9338 results for "cancer rna-seq"

in 33.35 milliseconds.

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620

• single-cell RNA-sequencing of human/mouse colonic crypts

  Human colonic stem cells are slow cycling compared with murine rapid cycling stem cells. Our study aims to identify slow cycling stem cell in human normal colon in vivo and to analyze gene signatures among rapid cycling stem cells, slow cycling stem cells and secretory progenitor cells using single cell RNA-seqencing . We further investigated in vivo dynamics of human colonic stem cell using patient-derived gene-enginered organoids and orthotopic xenotransplantation.

  Study JGAS000550

• Total RNA sequencing of 32 chronic lymphocytic leukemia (CLL) patients

  Peripheral blood mononuclear cells (PBMC) of CLL patients were isolated by density-gradient centrifugation over Linfosep (Biomedics, Madrid, Spain). B cells were purified with a CD19+ magnetic-bead system (MidiMACS, Miltenyi Biotec, Bergish Gladbash, Germany) according to the manufacturers’ instructions. Mean B-cell purity was >99% and the mean percentage of CD5+/CD19+ cells after purification was >98%, as measured by flow cytometry. Total RNA was extracted from purified cells in a single step using TriPure Isolation Reagent (Roche Applied Science, Vilvoorde, Belgium).Whole transcriptome sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Libraries underwent 2 × 76 bp paired-end sequencing on a HiSeq 2500 instrument (Illumina). The median number of paired-end reads was 60.5 million (range, 49.7-79.7 million).

  Dataset EGAD00001004047

• RNA-sequencing of a representative cohort of 209 AML cases

  Sample libraries were prepped using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned against the human genome (hg19) using STAR v2.5.4b2.

  Dataset EGAD00001007581

• RNA sequencing data of in vitro differentiated megakaryocyte cells transduced with E527K and WT SRC

  RNA sequencing data of in vitro differentiated megakaryocyte cells transduced with E527K and WT SRC. CD34+ hematopoietic stem cells (HSC) were isolated from healthy controls before transduction with WT-SRC and E527K-SRC lentiviral vectors in triplicate and differentiation to MK. Three replicates each of two pools were generated for both WT and E527K SRC transduced cells, resulting in 3 WT pool 1 samples, 3 WT pool 2 samples, 3 E527K pool 1 samples and 3 E527K pool 2 samples for a total of 12 samples. RNA was extracted and sequenced with following parameters: Platform: Illumina HiSeq4000, Library Prep Kit: TruSeq stranded mRNA, Sequencing Kit: Illumina HiSeq4000 100 cycles (76-8-8-7), Fragments: single end / fr-firststrand.

  Dataset EGAD00001008356

• An IL-1β driven neutrophil-stromal cell axis fosters a BAFF-rich microenvironment in multiple myeloma

  This depository contains data from two bulk RNA sequencing experiments: 1) Bulk RNA sequencing data of peripheral blood neutrophils from healthy donors cultured with a) human adipose-derived stromal cells (ADSC) as a model for mesenchymal stromal cells (MSC), and b) IL-1β stimulated ADSC as a model for inflammatory MSC as found in multiple myeloma (MM). 2) Bulk RNA sequencing data from ADSCs cultured a) without stimuli, b) with recombinant human IL-1β, c) with supernatant from iMSC-like cells, d) with neutrophils previously cultured with MSC, e) with neutrophils previously cultured with iMSC, f) with neutrophils previously cultured with iMSC in the presence of anti-human IL-1β or g) with neutrophils previously cultured with iMSC in the presence of an isotype control.

  Dataset EGAD00001010080

• Dataset that contains analyses of submission 14

  Description of analyses dataset of submission 14

  Dataset EGAD50000000045

• ChIP_3PEAKS

  Third batch of ChIP-seq narrowPeaks. Software: MACS2 v2.1.2

  Dataset EGAD00010002155

• Dataset that contains analyses of submission 15

  Description of analyses dataset of submission 15

  Dataset EGAD50000000083

• Single cell analyses of transcriptome and epigenome in neuroblastoma infiltrated bone marrow

  We report transcriptional and genome-wide ATAC-seq analyses at single cell resolution of 16 bone marrow samples with and without neuroblastoma infiltration. Our samples span across several neuroblastoma models, including MYCN amplified, ATRX mutated, and sporadic (lacking either alteration).

  Study EGAS00001006106

• BLUEPRINT release August 2014, ChIP-Seq for CD14-positive, CD16-negative classical monocyte

  ChIP-Seq data for 9 CD14-positive, CD16-negative classical monocyte sample(s). 59 run(s), 55 experiment(s), 55 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001000913

• BLUEPRINT release August 2014, ChIP-Seq for alternatively activated macrophage

  ChIP-Seq data for 4 alternatively activated macrophage sample(s). 29 run(s), 28 experiment(s), 28 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001000938

• BLUEPRINT release August 2014, ChIP-Seq for CD8-positive, alpha-beta T cell

  ChIP-Seq data for 2 CD8-positive, alpha-beta T cell sample(s). 13 run(s), 13 experiment(s), 13 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001000936

• BLUEPRINT release August 2014, ChIP-Seq for CD4-positive, alpha-beta T cell

  ChIP-Seq data for 3 CD4-positive, alpha-beta T cell sample(s). 21 run(s), 21 experiment(s), 21 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001000925

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

  ChIP-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 13 run(s), 13 experiment(s), 13 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 EGAD00001001136

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

  ChIP-Seq data for 7 CD4-positive, alpha-beta T cell sample(s). 46 run(s), 45 experiment(s), 45 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 EGAD00001001147

• snRNA-seq in white matter post-mortem tissue from MS and controls

  This Dataset is currently hosted by the European Nucleotide Archive. To access the data contained within the Dataset please follow the link below: https://www.ebi.ac.uk/ena/browser/view/PRJEB39323 Dataset consists of 20 snRNA-seq bam files from 10X v2. 5 samples from postmortem white matter tissue from non-neurological controls and15 samples from different MS lesions from the white matter tissue of 4 postmortem progressive MS patients.

  Dataset EGAD00001004544

• BLUEPRINT release August 2016, ChIP-Seq for Acute Lymphocytic Leukemia - CTR, on genome GRCh38

  ChIP-Seq data for 1 Acute Lymphocytic Leukemia - CTR sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002280

• BLUEPRINT release August 2016, ChIP-Seq for monocyte - None, on genome GRCh38

  ChIP-Seq data for 3 monocyte - None sample(s). 17 run(s), 17 experiment(s), 17 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002279

• BLUEPRINT release August 2016, ChIP-Seq for plasma cell, on genome GRCh38

  ChIP-Seq data for 5 plasma cell sample(s). 24 run(s), 23 experiment(s), 23 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002281

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MC2884 (24h), on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 (24h) sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002312

• BLUEPRINT release August 2016, ChIP-Seq for alternatively activated macrophage, on genome GRCh38

  ChIP-Seq data for 7 alternatively activated macrophage sample(s). 50 run(s), 49 experiment(s), 49 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002317

• BLUEPRINT release August 2016, ChIP-Seq for neutrophilic myelocyte, on genome GRCh38

  ChIP-Seq data for 4 neutrophilic myelocyte sample(s). 28 run(s), 23 experiment(s), 23 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002318

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - ATRA, on genome GRCh38

  ChIP-Seq data for 3 Acute Promyelocytic Leukemia - ATRA sample(s). 21 run(s), 20 experiment(s), 20 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002319

• BLUEPRINT release August 2016, Bisulfite-Seq for CD3-positive, CD4-positive, CD8-positive, double positive thymocyte, on genome GRCh38

  Bisulfite-Seq data for 2 CD3-positive, CD4-positive, CD8-positive, double positive thymocyte sample(s). 29 run(s), 2 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002325