11768 results for "cancer rna-seq"

in 27.64 milliseconds.

• Centroblast Cohort

  miRNA-seq Cohort of 15 Benign Centroblasts

  Dataset EGAD00001001075

• Rna_expression

  RNA expression microarray

  Dataset EGAD00010000869

• Lipomatous tumors with 12q amplification

  RNA sequencing of 20 tumors.

  Dac EGAC50000000036

• RNA sequencing of AD, MCI and control ONS cells

  Study EGAS00001006594

• The Extracellular RNA Quality Control (exRNAQC) study (phase 2)

  Study EGAS00001006499

• The Extracellular RNA Quality Control (exRNAQC) study (phase 1)

  Study EGAS00001005263

• Single cell transcriptional characterization of human megakaryocyte lineage commitment and maturation

  Single cell RNA-sequencing of sternal bone marrow reciding Hematopoietic Stem Cells (HSCs) and Megakaryocytes (MKs) from individuals undergoing elective open heart valve replacement. HSCs were defined as Lineage-, CD34+, CD38-, CD45RA-, CD90+, CD49f+ cells. MKs where CD41a+, CD42b+ and ploidy was determined with Hoechst. A sternal bone marrow scraping was taken directly following median sternotomy using a Volkmann’s spoon. The sample was collected into an EDTA Vacutainer tube containing 1.8mg/ml EDTA. 4mL of Dulbecco’s phosphate buffered saline (PBS, Sigma) containing 10% human serum albumin (HSA, Gemini Bio Products) was added and the whole volume was resuspended by pipetting 2-3 times. The sample was then put on metallic thermal beads (ThermoFisher Scientific) at a temperature between 0-4°C and transported to the University of Cambridge for further processing. For HSC isolation the cells were stained with the following antibody cocktail: PECy5 conjugated anti-lineage specific antibodies: CD2 (BD), CD3 (BD), CD10 (BD), CD11b (BD), CD11c (BD), CD19 (BD), CD20 (BD), CD56 (BD), biotinylated CD42b (Pab5, NHS Blood and Transplant, International Blood Group Reference Laboratory [IBGRL]), biotinylated GP6 (Pab5, NHS Blood and Transplant, International Blood Group Reference Laboratory [IBGRL]) used in combination with PECy5 conjugated streptavidin (Biolegend). Alexa Fluor 700 conjugated anti-CD34 (BD), PerCP-Cy5.5 conjugated anti-CD38 (BD), Pacific Blue conjugated anti-CD45RA (Invitrogen), PECy7 conjugated anti-CD90 (BD),PE conjugated anti-CD49f (BD). After staining cells were kept at 4°C before sorting using a FACS Aria Fusion flow sorter (BD). Single HSCs defined as Lineage-, CD34+, CD38-, CD45RA-, CD90+, CD49f+ cells were sorted by FACS directly into individual wells of a 96-well plate. Index sort data was collected for each single cell. For MK isolation the cells were stained for surface MK markers with mouse anti-human CD41a APC conjugated antibody (BD) and mouse anti-human CD42b PE conjugated antibody (BD) and for ploidy analysis with 1ug/ml Hoechst 33342 (Invitrogen). After incubation at 37°C for 30 minutes, the cells were kept at 4°C before sorting using a FACS Aria Fusion flow sorter (BD). Single cells and MK pools of 20 cells were sorted by FACS according to ploidy level using a 100uM nozzle directly into individual wells of a 96-well plate. cDNA synthesis and poly(A) enrichment was performed following the G&T-seq protocol (Macaulay et al. 2015), a variation of the Smart-seq2 protocol1. ERCC spike-in RNA (Ambion) was added to the lysis buffer in a dilution of 1:4,000,000.

  Dataset EGAD00001006677

• scRNA-seq of glioblastoma cells alone or after co-culture with cerebral organoid cells

  Dataset EGAD00001005315

• ChIPseq data

  ChIPseq data for CLL patients

  Dataset EGAD00001008665

• Dataset of PPB

  Whole exome sequencing and miRNA-seq data of PPB.

  Dataset EGAD00001000822

• ChIPseq data

  ChIPseq data for H3K4me1 and H3K9me3 in HT29; H3K4me1, H3K27me3, H3K9me3, H3K36me3 in LoVo.

  Dataset EGAD00001003258

• Covid19 Transcriptomic Data analysis in Irish Population

  The Samples were collected from Saint James's Hospital, Dublin and after informed consent. RNA-Sequencing library preparation was performed using the Illumina TruSeq Stranded Total RNA Library Prep Globin kit (20020612) with an input amount of 100 – 1000 ng. Library preparation was automated and processed using a Hamilton NGS Star. Library quality was assessed using the Roche KAPA Library Quantification Kit (7960298001) and GX Caliper HS Assay (CLS760672, 760517), run on Roche Lightcycler 480 II and Perkin Elmer LabChip GX Touch analyser respectively. Libraries were pooled and sequenced (75bp PE) on an Illumina NovaSeq 6000 instrument using NovaSeq 6000 S2 Reagent Kit v1.5 (20028314) targeting 50M paired reads. Raw data (BCL format) were demultiplexed and converted to FASTQ format using BCL2FastQ (Illumina). Adapters were trimmed using Skewer (PMID: 24925680) and QC assessed using FASTQC. STAR (PMID: 23104886) was used to align reads to the reference genome (GRCh38/hg38) as well as to the transcriptome (GENCODE v. 25). Quality of the RNA alignment was assessed using Picard QC. Gene and isoform quantification was performed using RSEM (PMID: 21816040). The study shares expression data (gene.results) and chimeric.junction.out.

  Study EGAS00001007116

• Phase I Clinical Trial Describing the Pharmacogenomics of Aspirin

  The study protocol for both cohorts has been previously described (Journal of Thrombosis and Thrombolysis 2012:1-12). HV1 cohort: Briefly 50 healthy volunteers were exposed to two weeks of 325mg/day aspirin after which whole blood RNA was collected in PAXgene tubes and profiled by microarray before and after aspirin exposure. The pre-aspirin samples were profiled on the U133A 2.0 array and the post-aspirin samples were profiled on the U1333plus 2.0 array. HV2 cohort: Briefly 53 healthy volunteers were exposed to four weeks of 325mg/day aspirin after which whole blood RNA was collected in PAXgene tubes and profiled by U133plus 2.0 array before and after aspirin exposure.

  Study phs000548

• Metatranscriptomic Sequencing of Pulmonary Fluid in Immunocompromised Children

  Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. In version 1.0 of this study, we performed RNA-based next generation sequencing (mNGS) on 41 lower respiratory samples collected from 34 children. We identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Potential pathogens were detected in half of samples previously negative by clinical diagnostics. In version 2.0, we included an addition 278 samples from 229 pediatric stem cell transplant patients with pulmonary disease.

  Study phs001684

• Impact of cryopreservation on transcriptome analysis of peripheral blood mononuclear cells

  To investigate the effect of cryopreservation on PBMCs, we conducted an experiment using samples from three healthy donors under four conditions: fresh PBMCs, PBMCs subjected to a single freeze–thaw cycle, PBMCs refrozen in freezing mix, and PBMCs refrozen in TRIzol. This resulted in a total of 12 samples (three replicates per condition). RNA was extracted from all PBMC samples using the Qiagen miRNeasy Mini Kit, followed by polyA RNA sequencing on the Illumina NovaSeq 6000 platform. Blood was collected from one male and two female adult donors. Sequencing yielded high-quality data, with an average of 27.8 million reads per sample and over 94% of bases exceeding a Q30 quality score.

  Study EGAS50000001196

• Exome and RNA sequencing data from 32 ocular and extraocular sebaceous carcinomas

  Sebaceous carcinomas (SeC) are cutaneous malignancies that, in rare cases, metastasize and prove fatal. Here we report whole exome sequencing on 32 SeC, revealing distinct mutational classes that explain both cancer ontogeny and clinical course. A UV-damage signature predominated 10/32 samples, while 9 were instead defined by microsatellite instability (MSI) mutations. UV-damage SeC exhibited poorly differentiated, infiltrative histopathologycompared to MSI signature SeC (p = 0.003), features previously associated with dissemination. Strikingly, UV-damage SeC transcriptomes and anatomic distributionclosely resembling those of cutaneous squamous cell carcinomas (SCC), implicating sun-exposed keratinocytes as a cell of origin. Like SCC, this UV-damage subclass harbors a high somatic mutation burden with >50 mutations/Mb, predicting immunotherapeutic response. In contrast, ocular SeC acquire far fewer mutations without a dominant signature, but show frequent truncating mutations in the ZNF750 epidermal differentiation regulator. Our data exemplify how different mutational processes convergently drive histopathologically related but clinically distinct cancers.

  Study EGAS00001002869

• Bulk RNAseq of cultured fibroblasts

  Fastq files from bulk RNAseq of fibroblasts after culture and facs sorting (N=9). Sorted FAP+ CAF cells RNAs were extracted using Qiagen miRNeasy Kit (Qiagen, #217004) according to the manufacturer's instructions. Verification of RNA integrity and quality was performed using the Agilent RNA 6000 nano Kit (Agilent Technologies, #5067-1511). cDNA libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina, #20020594) followed by sequencing on NovaSeq (Illumina).

  Dataset EGAD50000000323

• RNAseq of preneoplasia lung adenocarcinoma

  RNA sequencing of 168 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=38), adenocarcinoma in situ (AIS, N=22), minimally invasive adenocarcinoma (MIA, N=19) and invasive lung adenocarcinoma (ADC, N=38) and adjacent lung tissues (Normal, N=62).

  Study EGAS50000000271

• Blood Handling and Leukocyte Isolation Methods Impact the Global Transcriptome of Immune Cells

  In order to characterize the effects of upstream sample handling on the transcriptome of isolated leukocyte populations, we simulated various sample handling methods on whole blood prior to leukocyte isolation for low-input RNA-sequencing.

  Study phs001563

• The Normal Human Tissue Sequencing Project: Non-Diseased, Non-Malignant Tissues

  The Normal Human Tissue Sequencing Project provides RNA expression and DNA methylation data from normal (non-diseased) human tissues. This data set from a variety of source tissue is a valuable resource for human disease studies.

  Study phs000819

• Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression (non-hipo)

  This dataset contains 115 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

  Dataset EGAD50000001097

• Single cell RNA sequencing of co-culture of human organoids with polarized pro-inflammatory (M1) or anti-inflammatory (M2) macrophages

  In order to know if the mechanisms we identified in mice – demonstrating that macrophages are able to orchestrate the intestinal regenerative process – are conserved in humans we develop a co-culture system with human intestinal organoids and human polarized macrophages. We co-culture human organoids with pro-inflammatory or anti-inflammatory macrophages for 48h. On day 3 cells were collected to perform single cell RNA sequencing.

  Dac EGAC50000000270

• Whole-transcriptome sequencing of tumor samples

  Whole transcriptome sequencing of RNA samples from tumor samples of patients in the Neo-Pembro trial. For each patient, up to three samples were sequenced; one tumor biopsy at baseline, one tumor biopsy after induction chemotherapy, and a tumor sample from resection material at cytoreductive surgery. RNA was obtained from fresh-frozen samples where possible, or formalin-fixed paraffin-embedded when no fresh-frozen sample was available.

  Dataset EGAD50000001151

• Effects of KSP inhibitor filanesib in aggressive hepatoblastoma PDX cells

  Aim of this RNA sequencing dataset has been to asses effects caused by the KSP inhibitor filanesib in aggressive hepatoblastoma PDX cells. Two cell lines (HB-279 and HB-284) were utilised. DMSO-treated cells were used as controls.

  Study EGAS50000000899

• Comparison clinical recommendation MASTER and panel sequencing: RNA data

  This dataset contains 19 case/control samples of RNA sequencing data. Sequencing was performed on Illumina HiSeq 4000 and NovaSeq 6000 using TruSeq Stranded mRNA Kit. The sequencing was always paired.

  Dataset EGAD50000000625

• RNAseq

  Libraries for sixty-eight cases (23 EATL and 45 MEITL) were prepared starting from 1 µg of total RNA using the TruSeq Stranded total RNA Gold kit from Illumina (San Diego, California, USA) and were sequenced in three batches on a HiSeq 4000 machine from Illumina with an average output of 63 million reads per sample (range 49-126).

  Dataset EGAD50000001619

• B cells (CD19) RNAseq dataset of JIA patients with known uveitis status.

  CLUSTER consortium RNA sequencing dataset from UK JIA patient cohort with documented uveitis status. Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples and cryopreserved. Samples were subsequently thawed and flow-sorted for CD19+ B cells prior to RNA sequencing. Clinical metadata includes patient demographics and uveitis status at time of sampling.

  Dataset EGAD50000001616

• RNAseq of human intestinal epithelial cell layers cultured in OGM, ENR, and ENRRT

  This dataset contains RNA sequencing data in fastq and bam format from 24 samples of human jejunum organoids grown in 3D configuration or as 2D monolayers on anodisc imaging chambers (AICs) in medium formulations OGM, ENR, and ENRRT. The RNA sequencing samples were sequenced using paired-end sequencing (2x150 bp) on an Illumina NovaSeq 6000 instrument at the SciLifeLab National Genomics Infrastructure (NGI) in Uppsala.

  Dataset EGAD50000001766

• Comprehensive molecular and clinicopathological profiling of desmoid tumors

  Previous studies have not clearly identified a prognostic factor for desmoid tumors (DT). Whole-exome sequencing and/or RNA sequencing were performed in 64 cases of DT to investigate the molecular profiles in combination with the clinicopathological characteristics.

  Study JGAS000270

• Genome-wide integrative analysis of pediatric pancreatoblastoma

  Pancreatoblastoma is the most common pancreatic malignancy of young children, but its molecular pathogenesis remains poorly understood. To understand the molecular pathogenesis of pancreatoblastoma, we comprehensively analysed the whole exome sequencing, RNA sequencing, SNP array, and methylation array data of pancreatoblastoma.

  Study JGAS000088

• Integrated genetic and epigenetic analysis of myxofibrosarcoma

  Myxofibrosarcoma (MFS) is a common histological subtype of adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high propensity for local recurrence. We underwent whole exome sequencing, RNA sequencing, and methylation analysis of MFS.

  Study EGAS00001002889

• Gene_epression_regulation_in_cytokine_induced_immune_cell_states

  We isolated T cells and monocotyes from healthy platelet donors and cultured them in resting and stimulated conditions with addition of a range of cytokines. We performed RNA sequencing to assess impact of different disease-relevant cytokines upon immune cell responses.

  Study EGAS00001003823

• Potent neutralizing antibodies against SARS-CoV-2

  The COVID-19 pandemic urgently needs therapeutic and prophylactic interventions. Here we report the rapid identification of SARS-CoV-2 neutralizing antibodies by high-throughput single-cell RNA and VDJ sequencing of antigen-enriched B cells from 60 convalescent patients.

  Study EGAS00001004412

• HLF COPD Transcriptomics

  We generated transcriptomes of primary human lung fibroblasts (HLFs) isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease. RNA sequencing analysis demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization.

  Study EGAS00001006602

• Transcriptomic analysis of MYC overexpression in LT-HSC.

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors (empty E CTRL or MYC). Six days after transduction, BFP+ transduced cells were sorted for RNA extraction and sequencing

  Study EGAS00001004970

• Isoform-level profiling of m6A modifications in human brain

  Oxford Nanopore direct RNA sequencing (DRS) can quantify isoform expression, modifications and polyA tail lengths, enabling simultaneous investigation of the transcriptome and epitranscriptome. We applied DRS to three post-mortem human brain regions: prefrontal cortex, caudate nucleus and cerebellum.

  Study EGAS00001007742

• Human Biofluid RNA Atlas

  This dataset contains small RNA sequencing data and mRNA capture sequencing data from 20 different human biofluids (amniotic fluid, aqueous humor, ascites, bile, bronchial lavage fluid, breast milk, cerebrospinal fluid, colostrum, gastric fluid, pancreatic cyst fluid, plasma, saliva, seminal fluid, serum, sputum, stool, synovial fluid, sweat, tear fluid and urine). In total, 180 samples were sequenced. Files are provided in fastQ format. Samples were sequenced on a NextSeq 500.

  Dataset EGAD00001005439

• TSGKO_RNASeq

  Libraries were prepared from RNA-extracted cell lines using Illumina RNA library prep kit. Samples were sequenced on Illumina HiSeq 4000 or HiSeq 2500.

  Dataset EGAD00001008559

• Circular RNA characterization in functionally distinct brain regions

  RNA extracted from middle temporal gyrus (MG) brain region of healthy elderly controls. Three pairs of samples were generated, each pair consisting of one sample that was enriched for circular RNAs using RNase R, and a second sample that was not enriched (total N=6). Remaining samples in the study from other functionally distinct brain regions are currently under process and will be released soon.

  Dataset EGAD00001004211

• RNAseq_pituitary_adenoma

  Total RNA was extracted using RNAble (Eurobio), cleaned-up with RNeasy columns (Qiagen) and sequenced. The libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq Stranded mRNA protocol (Illumina), starting from 1 µg of high quality total RNA. Paired end (2 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on hg19 (GRCh37) human reference genome with STAR (v.2.5.2a)

  Dataset EGAD00001004996

• RNA-sequencing of six Pilocytic astrocytoma tumors

  Total stranded TruSeq RNA sequencing by Illumina of six tumor samples from six cases of pediatric Pilocytic astrocytoma. The data is published in the following paper: Tomic TT, Olausson J, Wilzen A, Sabel M, Truve K, Sjogren H, Dosa S, Tisell M, Lannering B, Enlund F, Martinsson T, Aman P, Abel F. A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PLoS One. 2017 Apr 27;12(4):e0175638.

  Dataset EGAD00001003143

• Peripheral blood RNA-sequencing in 4,732 participants of the INTERVAL cohort

  We performed bulk RNA-sequencing on peripheral blood collected from 4,732 blood donors recruited as part of the INTERVAL study. Using these data, we mapped gene expression and splicing quantitative trait loci (QTLs). Then, we integrated these data with protein, metabolite and lipid QTLs in the same individuals. The study aimed to identify the shared genetic etiology across transcriptional phenotypes, molecular traits and health outcomes in humans.

  Dataset EGAD00001008015

• oncogenic gene fusions in primary colon cancers

  This dataset represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. RNA-sequencing was performed using TruSeq library preparation and samples were sequenced on Illumina NextSeq and HiSeq. The data are available as Illumina NextSeq and HiSeq fastq files (_R1.fastq and _R2.fastq for each tumor sample, 556 files in total).

  Dataset EGAD00001003291

• RNA-sequencing data from human FSHD and control skeletal muscle biopsies

  This project includes RNA-sequencing data from human FSHD and control skeletal muscle biopsies. This project includes data from 28 FSHD patients (total 37 samples, including vastus lateralis and tibialis anterior muscles) and 12 control individuals (total 24 samples, including vastus lateralis and tibialis anterior muscles).

  Dataset EGAD00001008337

• Exome and RNA-sequencing data from a relapsed t(1;19) acute lymphoblastic leukemia

  Sequence data is from 4 samples from an adult patient with TCF3-PBX1 t(1;19)-positive acute lymphoblastic leukemia. Exome sequencing was performed on a skin biopsy (normal tissue control) and leukemic bone marrow biopsies taken at diagnosis and at two relapse time points. RNA-sequence data is from leukemic bone marrow from two relapse biopsies.

  Dataset EGAD00001002203

• RNA sequencing of cytokine-induced T cell responses

  Cytokines affect T cell responses by polarising them to different phenotypes. We isolated T cells from healthy platelet donors and cultured them in resting and stimulated conditions, as well as in the presence of Th1, Th2, Th17 and iTreg cocktail. In addition, T cells were stimulated in the presence of IL-10, IL-21, IL-27, IFNb and TNFa. We performed bulk RNA sequencing to assess impact of different disease-relevant cytokines upon T cell response.

  Dataset EGAD00001005291

• RNA-sequencing and targeted DNA-sequecing of human thyroid tumors and normal samples

  RNA-sequencing data: 5 normal thyroid tissues, 14 papillary thyroid carcinomas, 2 lymph node metastases, 19 poorly differentiated thyroid carcinomas and 17 anaplastic thyroid carcinomas; Targeted DNA-sequencing of the 165 genes included in the “Solid and Haematological tumors” panel (BRIGHTCore, Brussels, Belgium): 2 normal thyroid tissues, 2 poorly differentiated thyroid carcinomas and 7 anaplastic thyroid carcinomas; 2 FASTQ files for each sample (paired).

  Dataset EGAD00001011678

• Improved Sezary cell detection and novel insights into immunophenotypic and molecular heterogeneity in Sézary syndrome

  We performed a prospective investigation in Sézary syndrome by the application of a standardized multiparameter flow cytometry, FACS-cell sorting, and RNA-sequencing for an in-depth immunophenotypic and transcriptional profiling of Sézary cells.

  Study EGAS00001005229

• RNA sequencing of primary B-cells infected with EBV virus

  Study EGAS00001007187

• Total RNA-Sequencing of patient-derived xenograft models of myxoid liposarcoma

  Study EGAS00001004901