12213 results for "cancer rna-seq"

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• Bulk and Single-Nuclei RNA-seq with ATAC-seq of Breast Tumors Pre- and Post-Palbo ciclib/Endocrine Therapy

  This dataset comprises bulk and single-nuclei multiomic profiles from patients with ER+/HER2- early breast cancer enrolled in the NeoRHEA phase 2 trial. The bulk RNA-seq component includes 78 pre-treatment and 49 post-treatment tumor samples from 97 patients. The single-nuclei component includes matched pre- and post-treatment samples from 37 patients, totaling 63 samples analyzed by simultaneous snRNA-seq and snATAC-seq. Combined, the data contains bulk transcriptional profiles and single-nuclei gene expression/chromatin accessibility matrices for over 226,000 high-quality nuclei, encompassing tumor, immune, and stromal cells. Technologies used include Illumina NovaSeq 6000 for sequencing and the 10x Genomics Chromium platform (Multiome kit for single-nuclei, standard RNA library prep for bulk).

  Dataset EGAD50000002038

• single cell RNA-seq data of 10 small cell lung cancer patients

  This dataset contains 10 paired fastq files sequenced on Illumina NextSeq 550 sequencer. Tumors were rapidly dissociated after the surgical procedure using the Miltenyi Biotec Human Tumor Dissociation kit (cat# 130-095-929). Libraries were constructed using the VDJ NextGEM v1.1 10x Genomics Chromium kit. Single cell RNA-seq analysis was performed using Seurat R package.

  Dataset EGAD50000002034

• GELATO clinical trial RNA-Seq data (primary tumors and local recurrences)

  RNA-Seq data of 10 lobular breast cancer primary tumors and 3 local recurrences obtained from 11 unique patients from GELATO clinical trial. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from archived FFPE material.

  Dataset EGAD00001009835

• Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types

  Raw bam file for bulk RNA-seq of checkpoint-blockade treated lung cancer cohorts

  Dataset EGAD50000000469

• RNA sequencing of in vitro generated suppressive myeloid cells using parental and Sialidase expressing A549 cancer cell lines

  Fresh peripheral blood mononuclear cells of four human donors were cultured together with either lung adenocarcinoma A549 cancer cells or A549-expressing H1N1 Sialidase cancer cells. These treatments induced the differentiation of donor cells into immunosuppressive MDSC-like cells, which were further subjected to bulk RNA sequencing. RNA-seq TruSeq libraries were generated from polyA-enriched mRNA isolated from the samples, and sequenced in paired-end mode on 4 lanes of an Illumina NextSeq 500 flow-cell

  Dataset EGAD00001012437

• Gene expression analysis of clear cell renal cell carcinoma

  To identify genes that are differentially expressed across different conditions (cancer vs normal, normoxic vs hypoxic), we performed RNA-seq in 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions.

  Study EGAS50000001324

• Bulk RNA-seq of human muscle-invasive bladder cancer tissue samples before and after platinum-based chemotherapy (Chelushkin, van Dorp, et al., 2024)

  The current dataset represents bulk RNA-Seq gene expression profiling (with an exome library preparation kit) of muscle-invasive bladder cancer tissue samples obtained before and after platinum-based chemotherapy. 89 samples are pre-treatment transurethral resection of the bladder tumor (TUR-BT) tissue at diagnosis (baseline), 86 are post-treatment cystectomy tissue (resected tumor bulk), comprising 76 pairs of samples from the same patients. FASTQ files contain gene expression data.

  Dataset EGAD50000000446

• DAC for CTOS colorectal cancer organoids

  This Data Access Committee (DAC) is responsible for reviewing and approving access requests to controlled-access human sequencing data generated from colorectal cancer patient-derived organoids established using the CTOS method. The dataset includes whole-exome sequencing (WES) and RNA sequencing (RNA-seq) data. Access requests are evaluated for consistency with the original informed consent and the approved research purposes.

  Dac EGAC50000000915

• Bulk RNA sequencing of metastatic colorectal cancer patient-derived xenografts with known response to irinotecan

  Standard polyA enriched RNA-seq profiles of patient-derived xenograft (PDX) models from NOD/SCID mice without treatment. These PDX are obtained from tumors from patients with metastatic colorectal cancer after serial passaging in mice.

  Dataset EGAD50000002138

• Integrated Exome and RNA Sequencing of Dedifferentiated Liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000177

• Genomic Changes in Breast Cancer Among Chinese Women in Hong Kong

  Recently, tumor sequencing and profiling analyses have improved molecular classification and refined existing breast cancer subtypes. However, epidemiologic data are absent in most somatic profiling studies even in extensively studied Western populations. The expansion of genomic studies to understudied populations with the integration of etiologic factors will allow the capture of a much wider range of genetic structure and mutagenic exposures associated with breast cancer risk. We therefore conducted a detailed molecular characterization of paired breast tumor/normal tissues using fresh frozen tissues collected from breast cancer cases in an ongoing breast cancer case-control study in Hong Kong. These analyses included whole genome (WGS)/exome sequencing (WES), targeted DNA panel sequencing, RNA sequencing (RNA-Seq), and genome-wide methylation profiling analyses.

  Study phs001870

• RNA-Seq Data From Early Stage Triple Negative Breast Cancer Tumors Treated With TVEC and Chemotherapy (MCC18621)

  This study is a phase 1/phase 2 trial testing the combination of talimogene laherparepvec (TVEC) and neoadjuvant chemotherapy for the treatment of stage II-III triple negative breast cancer. The trial demonstrated that the addition of TVEC to neoadjuvant chemotherapy was feasible, and resulted in a pathological complete response (pCR) rate of 45.9%, residual cancer burden (RCB) 0-1 rate of 65%, and event free survival of 89%. The macrodissected formalin-fixed paraffin-embedded (FFPE) samples were from 50 patients treated across two phases at different timepoints (pre-treatment, 6th week of treatment, and surgical resection). RNA-Seq data is provided along with clinical classifiers.

  Study phs003199

• Clinical phenotype data

  Clinical data corresponding to the patients with ovarian cancer studied using scRNA-seq and bulk RNA-seq. Variables include molecular subtype, predicted immune phenotype, reviewing pathologist comment, final immune phenotype, histology characterization, and tumor stage.

  Dataset EGAD00001006973

• RNA-seq data from 7 CAF-S1 primary cell lines isolated from breast Cancer

  Dataset EGAD00001006144

• MOSAIC Window Glioblastoma Data

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 10 Glioblastoma (GBM) Cancer patients. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001352

• Single-cell RNA-seq of murine splenocytes from Bcl6tg/+ and Cd70-/-; Bcl6tg/+ diffuse large B-cell lymphoma mouse models and Cd70-/- and wild-type controls.

  Study EGAS00001007570

• LOGGIC Core BioClinical Data Bank: Added clinical value of RNA-Seq in an international molecular diagnostic registry for pediatric low-grade glioma patients

  Study EGAS00001007072

• Whole Exome Sequencing of 60 tumor/normal matched liver Cancers (HCC)

  The French ICGC project on liver tumors is coordinated by Pr Jessica Zucman-Rossi and funded by Inca (French Institute for Cancer). The aim of the present project is to identify the catalog of somatic and germline mutations in liver tumors using whole genome (WGS) and whole exome sequencing (WGS), integrated with DNA methylation and RNA sequencing (RNA-seq) data. The present series corresponds to 60 whole exome tumor/normal pairs with matched RNA-seq.

  Dataset EGAD00001004180

• Acetalax and bisacodyl triple-negative breast cancer RNA-Seq

  Analysis of gene expression in triple negative breast cancer xenografts exhibiting good or bad response upon acetalax and bisacodyl treament.

  Study EGAS50000000618

• Results of RNA sequencing from all patients/samples

  Results of sequencing the targeted RNA-seq panel of breast cancer patients and controls. This dataset comprises of FASTQ files of 295 samples (both breast cancer patients and controls) and the results of mapping the FASTQ files to the reference human genome (hg38) available in a form of raw gene expression matrix.

  Dataset EGAD50000000017

• Multiregional single nuclei RNA-seq and WGS of prostate cancer

  This study investigates the clonal evolution and metastatic dissemination of prostate cancer using multiregional single-nuclei RNA sequencing (snRNA-seq) and low-pass whole-genome sequencing (WGS) data from 43 spatially distinct tumor areas in five patients with locally advanced prostate cancer, including both primary and regional lymph node samples. We employed the Chromium Next GEM Single Cell 3’ Kit (v3/3.1, 10x Genomics) for single-nuclei transcriptome profiling and constructed bulk WGS libraries using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs) from the same pool of nuclei extracted from each area. snRNA-seq data were aligned to the human genome (GRCh38-1.2.0_premrna) using 10x Genomics Cell Ranger v5.0.0, while WGS reads were aligned to the human reference genome (GRCh38) with BWA MEM, achieving an average sequencing depth of 0.3X for low-pass WGS and 16X after resequencing.

  Dataset EGAD50000001357

• Bulk RNA-seq of stromal cells from multiple cancer types

  We sorted CD45-CD44+CD90+ stromal cells from multiple tumor types and performed bulk RNA-sequencing.

  Dataset EGAD00001009176

• Gene Expression of Small Cell Carcinoma of the Ovary-Hypercalcemic Type (SCCOHT)

  Small cell carcinoma of the ovary-hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer afflicting young women at a median age of 24 years. SCCOHTs are characterized by loss of protein expression of SWI/SNF chromatin remodeling ATPases SMARCA4 and SMARCA2 through mutation and epigenetic silencing, respectively. This study aims to establish gene expression profiles of this cancer through RNA-Seq of fourteen pathologically confirmed cases of SCCOHT tumors.

  Study phs001528

• RNAseq of pre- and post-5AZA-treated head and neck cancer patients refractory to anti-PD-1 therapy

  RNA sequencing (RNA-seq) was performed on baseline (before low-dose 5-aza treatment) and on-treatment (low-dose 5-aza treatment for 5 or 10 days) tumor samples from eight participants with head and neck cancer who were refractory to anti-PD-1 therapy. RNA library preparations, sequencing reactions, and initial bioinformatics analyses were conducted at GENEWIZ, LLC. In total, 16 150-bp pair-end RNAseq data were generated.

  Dataset EGAD50000001010

• RNA sequencing data from patient derived colorectal cancer organoids

  This study aimed to develop NovumRNA, a bioinformatics pipeline designed to predict non-canonical tumor-specific antigens (ncTSAs) from human tumor RNA-sequencing data, potentially broadening the target pool for cancer neo-epitope-based immunotherapies. The pipeline was utilized to analyze RNA-seq data from ten patient-derived colorectal cancer (CRC) organoids, representing seven microsatellite stable (MSS) and three microsatellite instable (MSI) tumors. The goal was to explore the ncTSA landscape in CRC, particularly in MSS cases, which typically exhibit low tumor mutational burden and limited response to current immunotherapies. The study identified comparable ncTSA burdens across MSI and MSS tumors, suggesting new avenues for immunotherapy targeting non-canonical antigens in CRC. NovumRNA is available at: https://github.com/ComputationalBiomedicineGroup/NovumRNA.

  Study EGAS50000000685

• MOSAIC Window - Bladder dataset

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 15 Muscle-invasive Bladder Cancer patients, treated with upfront cystectomy. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000000967

• Sequencing data from the study "Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer"

  This dataset consists of 71 whole-genome samples and 47 RNA-seq samples. All WGS samples are provided in .bam format and RNA-seq samples are provided as .fq.gz (paired-end). Next-generation sequencing data on whole genomes were processed by aligning sequencing reads to a reference genome (NCBI build 37/hg19) using bwa-mem (0.7.13-r1126).

  Dataset EGAD50000001978

• MOSAIC Window Bladder Data

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 15 Muscle-invasive Bladder Cancer patients, treated with upfront cystectomy. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001251

• FFPE cohort with RNA-seq data of tumor samples

  This dataset contains RNA-seq raw data in fastq format from 14 tumor samples. The samples are from primary tumors or metastasis and represent various cancer entities. The samples are formalin-fixed paraffin-embedded (FFPE) treated. For target enrichment SureSelect XT Human All Exon V6 was used. The libraries were sequenced in paired-end mode (2 x 50 nt) on a NovaSeq6000 S2 flow cell.

  Dataset EGAD00001006781

• PanCurX Translational Research Initiative - RNA-Seq mapped and unmapped reads

  Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases - RNA-Seq mapped and unmapped reads

  Dataset EGAD00001004548

• RNA-seq from PDAC samples

  Bam and fastq files from RNA-seq of PDAC samples described in Transcription phenotypes of pancreatic cancer are driven by genomic events events during tumour evolution

  Dataset EGAD00001005799

• Breast Cancer TNBC Single-Cell RNA-Seq Dataset

  Single-cell RNA-Sequencing of five TNBC primary breast cancers from Wu et al. (2020) EMBO J study. Data was generated using the Chromium controller (10X Genomics) and sequenced on the NextSeq 500 platform.

  Dataset EGAD00001006981

• High-throughput sequencing data for study of molecular drivers of resistance to castration in localised prostate cancer

  Aligned whole-genome sequencing and RNA-seq of localised prostate cancer for study 'Loss of SNAI2 in prostate cancer correlates with clinical response to androgen deprivation therapy'.

  Dataset EGAD00001006640

• Analysis of genomic alterations in dedifferentiated liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000182

• Transcriptomic intra-tumor heterogeneity of colorectal cancer evaluated by RNA sequencing of multi-regional biopsies

  RNA sequencing of a total of 41 tumor biopsies taken from a total of 14 patients with colorectal cancer. Ribosomal RNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Illumina, CA, USA) and Paired-end sequencing were performed using ScriptSeq v2 RNA-seq Library preparation Kit (Illumina). Data processing of the paired raw sequence reads was performed using TopHat2, with mapping to the human reference genome HG19. Forty-one BAM files with reads mapping the the human reference genome (HG19) is enclosed.

  Dataset EGAD00001006636

• Breast Cancer Genome Guided Therapy Study (BEAUTY)

  The Breast Cancer Genome Guided Therapy Study (BEAUTY) is a prospective neoadjuvant clinical study enrolling 140 women with Stage I-III breast cancer. The goals of this study were to 1) perform comprehensive sequencing of germline and tumor tissues (exome and RNA seq), 2) identify genomic alterations and perturbed pathways associated with response/resistance to standard chemotherapy, and 3) develop patient-derived xenograft (PDX) for testing of therapeutic regimens chosen on the basis of alterations identified by genetic sequencing.

  Study phs001050

• snRNAseq prostate cancer

  single-nucleus RNA seq characterization of human fresh frozen prostate cancer samples and non-malignant controls for the same patients. Biopsies were sectioned in 100 micron thick sections, adjacent to those used for spatial transcriptomics.

  Dataset EGAD50000001633

• Transcriptomic profiling of prostate cancer metastasis xenograft models

  RNA-seq profiling of 2 prostate cancer xenograft mouse models, each at the intact state (n=3), castrated state (n=4) and castrated + AR replacement (n=3).

  Dataset EGAD00001006551

• RNA Sequencing Analysis of Patient-Derived Xenograft Tissue PIM-084 Treated with L-NMMA+Alpelisib vs Vehicle Control

  This dataset contains RNA-seq analysis of vehicle control compared to L-NMMA+alpelisib treated metaplastic breast cancer PDX PIM084 tumors (RNA sequencing and analysis performed by Novogene). The submitted data contains the gene ID, gene name, normalized read counts from all samples from control group and combination treatment group, log2-fold change derived from DESeq2 R/EdgeR package, p-value, adjusted p-value, read counts from each group, and gene FPKM from the each sample in the group. Due to patient privacy, we are submitting only the processed and desensitized RNA sequencing analysis to this repository.

  Study phs003814

• Multi-omics datasets (WES, RNA-seq) of mesothelioma MIST2 study, a phase II CDK4/6 (abemaciclib) clinical trial

  This study comprises 26 mesothelioma patients with whole exome and RNA sequencing, to to assess potential sensitivity to CDK4/6 inhibition in p16ink4A-negative mesothelioma.

  Study EGAS50000001823

• Peripheral clonal expansion of T cells (scRNA-seq)

  Single-cell RNA-seq of tumor-infiltrating lymphocytes from 14 cancer patients before treatment, taken from tumor, normal adjacent tissue, and peripheral blood. Dataset consists of paired-end FASTQ files, including replicate libraries and runs.

  Dataset EGAD00001005464

• Single-cell RNA-Seq of CAF-S1 sub-population of Fibroblast in breast Cancer tumors

  Dataset EGAD00001006163

• RNA-SEQ data from 13 CAF (Cancer Associated Fibroblast) samples sorted from fresh high-grade ovarian carcinoma

  Dataset EGAD00001003460

• FAM50A_Disruption_in_TOV21G_Cells___RNAseq

  In this project we aimed to assess the transcriptional consequences of disrupting FAM50A in TOV21G cells in vivo. To do this we generated a dox inducible FAM50A gRNA allele such that we could conditionally inactivate FAM50A by feeding mice a diet containing doxycycline. Tumour masses were harvested from mice when they reached the ethical limit and RNA was extracted for RNA-Seq analysis.

  Study EGAS00001004156

• Single-Cell ATAC and RNA Sequencing of Human Breast Cancer Reveals Salient Cancer-Specific Enhancers

  Matched single-cell chromatin accessibility sequencing (scATAC-seq) and single-cell transcriptomic sequencing (scRNA-seq) were performed for 12 human breast tumor samples, 4 normal human mammary reduction samples, and 4 human breast cancer cell lines (HCC1143, SUM149PT, MCF7, and T47D). Both scATAC-seq and scRNA-seq assays resolved the underlying cellular heterogeneity in chromatin accessibility and transcriptional output for each patient sample. In this work, we quantitatively linked variation in chromatin accessibility to gene expression across malignant and non-malignant cell types from patient samples. We then showed that our findings were recapitulated in the breast cancer cell line samples. These data will serve as an important resource for the single-cell genomics and breast cancer research communities.

  Study phs003253

• Transcriptome profiling for Korean Diffuse Gastric cancers

  Gastric cancers in young patients are aggressive and predominantly of diffuse histology. Also, they are more frequent in female. To identify transcriptome profile in this unique subset of gastric cancers, RNA-seq analyses were performed using frozen cancer tissue. Adjacent normal tissue of the same patients were used in differently expressed gene selection and fusion gene prediction.

  Study EGAS00001001859

• RNA seq data of 2 lung cancer samples prepared using 2 different RNA-seq library preparation protocols

  Raw data used for generation of the results in the Vardetector manuscript – “.bam” files of RNA-seq data of tumor samples of 2 patients prepared with 2 different library preparation protocols (exome-capture and ribodepletion –> 4 “.bam” files in total). The submission also contains the somatic mutations “.vcf” files (4 in total, however 2 unique). Moreover, also an output of the Vardetector module (“.csv” file with the number of reads above the mutations of interest) is present in the submission (4 “.csv” files in total).

  Study EGAS50000001419

• Colorectal cancer peritoneal metastasis

  This dataset consist of 72 samples profiled on whole exome sequencing and 94 samples profiled on whole transcriptome sequencing. The Agilent SureSelect Human All Exon v6 kit (Agilent Technologies) was used for whole exome sequencing. For RNA-seq experiments, library preparation was conducted using the Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit protocol (Illumina). Libraries were sequenced on a HiSeq4000 sequencer using the paired-end 150 bp read option. Sequences in cram format was provided.

  Dataset EGAD50000001199

• Raw RNA-seq data for clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint. This dataset includes the raw RNA-seq data.

  Dataset EGAD00001006205

• Genomic and Transcriptomic Data from Advanced Rare Cancer Patients Treated with Pembrolizumab

  This dataset comprises whole exome sequencing data and RNA-seq data of advanced rare cancer patients.

  Dataset EGAD50000002182