3924 results for "RNA AND sequencing OR transcriptome"

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• RNA-seq of frontal post-mortem human brain tissue

  RNA-sequencing dataset of post-mortem human brain tissue of FTD patients with mutations in GRN, MAPT and C9orf72 and healthy controls.

  Dataset EGAD00001008014

• Bulk RNA-seq of Human Epiglottis and Subglottis

  This study contains bulk and single nucleus RNA-seq of human epiglottis and subglottis tissue.

  Dataset EGAD50000001278

• Single nucleus RNA-seq of human epiglottis and subglottis

  This dataset contains single nucleus RNA-seq of human epiglottis and subglottis tissue performed using the 10X platform

  Dataset EGAD50000001279

• RNA-seq in insulinomas

  RNA-seq datasets in human insulinoma samples

  Dataset EGAD50000000462

• Single Cell RNA-Seq

  Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq. Nine techniques applied to samples from four PDX models: #105, #177, #233, #264

  Dataset EGAD50000000216

• 7 samples RNA-seq raw data

  Dataset comprising raw paired RNA-seq data in fastq.gz format for 7 samples of rosette forming brain tumors

  Dataset EGAD00001009265

• RNA-seq data from sorted CML and normal samples

  RNA-seq data from sorted populations from 10 CML samples and 4 normal bone marrow samples.

  Dataset EGAD00001004079

• Glioblastoma stem cell lines RNA-seq

  RNA-seq data for three Glioblastoma stem cell (GSC) lines exposed to PRMT5 inhibitor and control samples.

  Dataset EGAD00001006095

• RNA-seq of UTUC samples

  This dataset includes transcription profiling by RNA-seq of 3 upper urinary tract urothelial tumours (UTUC).

  Dataset EGAD00001008138

• In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  Dataset EGAD00001009688

• bulk RNA-seq of the 5 HCC patients which also have the single cell T cell RNA-seq data

  bulk RNA-seq data of the 5 HCC patinets. Single cell RNA seq data of these patients was under the accession number EGAD00001003337

  Dataset EGAD00001004148

• IVAC Melanoma

  Whole exome and transcriptome sequencing of 12 melanoma patients (including technical replicates). linicalTrials.gov Identifier: NCT02035956. Paper: Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer - Nature volume 547, pages 222–226

  Dataset EGAD00001004455

• Integrated Multiomics Uncovers Distinct Macrophage Alterations in Human Metabolic dysfunction-Associated Steatohepatitis Progression

  We report single-nuclei RNA sequencing data from human livers in metabolic dysfunction-associated steatotic liver disease (MASLD) patients.

  Study EGAS50000000768

• Hematological toxicity following CAR-T cells injection dataset

  This dataset containes 44 paired of bulk RNA sequencing and 42 parired of single cell RNA sequencing issued from bone marrow aspirations obtained from patients treated with CAR-T (CD3+, CAR T+, CD34+ sorted populations).

  Dataset EGAD50000001142

• Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA-sequencing the pros and cons

  RNA sequencing data of a collection of 6 pediatric ependymoma cases

  Dataset EGAD00001009301

• RNA-Seq data for manuscript titled: CBL0137 impairs homologous recombination repair and sensitizes high-grade serous ovarian carcinoma to PARP inhibitors Sequencing

  RNA-Seq data for manuscript titled: CBL0137 impairs homologous recombination repair and sensitizes high-grade serous ovarian carcinoma to PARP inhibitors Sequencing

  Dataset EGAD00001009799

• Single-cell RNA sequencing of RCC patients

  Single-cell RNA sequencing was performed on viable frozen tumor dissociated cells from three RCC patients. The raw data is available as fastq files.

  Dataset EGAD00001011045

• Additional RNAseq data of metastatic breast cancer samples

  Paired-end RNA sequencing data from 33 metastatic breast cancer samples. Sequencing was performed on the Illumina NovSeq 6000 using NEBNext Single Cell and Low Input RNA Library Prep Kit for Illumina.

  Dataset EGAD00001015678

• Strand-specific RNA sequencing of 16 pairs of primary and relapsed IDH-wt glioblastomas

  This dataset contains strand-specific RNA sequencing data from 16 primary/relapsed sample pairs of IDH-wt glioblastomas

  Dataset EGAD00001004564

• RNA sequencing of adult T-cell leukemia/lymphoma

  RNA sequencing of 57 tumor samples of adult T-cell leukemia/lymphoma as well as 3 samples of HTLV-1 carrier and 3 samples of healthy volunteers.

  Dataset EGAD00001001411

• RNA sequencing data of high-grade serous ovarian cancer samples

  RNA sequencing data of over 200 HGSOC samples at diagnosis, after chemotherapy and during progression.

  Dataset EGAD00001006456

• Single cell RNA-sequencing of glioblastoma tumours

  Single cell RNA-sequencing of fresh glioblastoma tumor biopsies with 10x Genomics 3' expression (v2 chemistry). Aligned to GRCh38 reference genome using CellRanger.

  Dataset EGAD00001006803

• Single cell RNA-sequencing of glioblastoma stem cell lines

  Single cell RNA-sequencing of glioblastoma stem cell (GSC) lines with 10x Genomics 3' expression (v2 chemistry). Aligned to GRCh38 reference genome using CellRanger.

  Dataset EGAD00001006804

• Single nuclei RNA-sequencing of glioblastoma tumors

  Single nuclei RNA-sequencing of snap frozen glioblastoma tumor tissue with 10x Genomics 3' expression (v2 chemistry). Aligned to GRCh38 reference genome with intron using CellRanger.

  Dataset EGAD00001006802

• RNA sequencing upon depletion of RAF kinases vs. MAPK inhibition in KRAS mutant cells

  RNA Sequencing upon shRNA mediated depletion of RAF kinases or treatment with Cobimetinib (GDC-0973, 250nM, 6hrs) or with pan RAFi (AZ-628, 10uM, 6hrs)

  Dataset EGAD00001008384

• Patient-Derived Breast Cancer Organoid Study

  This study uses normal and tumor tissues from breast cancer patients to derive 3D cell culture models called organoids. Organoid technology is an innovative platform that can be used to study a patient's tumor in a dish ex-vivo. As part of this study we have comprehensively characterized these models using next-generation sequencing for: 1) pathogenic SNVs in a targeted gene panel 2) copy number alterations 3) transcriptome analysis using RNA sequencing and 4) single-cell RNA sequencing

  Study phs002722

• Deciphering Intratumoral Molecular Heterogeneity in Clear Cell Renal Cell Carcinoma with a Radiogenomics Platform

  We used 200 ccRCC samples from 51 tumors to simultaneously isolate DNA, RNA, and protein according to established protocol. RNA quality was assessed using an Agilent Bioanalyzer, and total RNA with RIN>7 was used for further RNA sequencing. 184 ccRCC samples from 49 tumors passing initial quality control underwent RNA sequencing at Admera Health Inc. (Genohub Inc., Austin, TX). RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA high throughput (HT) sample preparation kit following the manufacturers’ protocol. Pair-end RNA Seq data was deposited in this cohort.

  Dataset EGAD00001005356

• SAPCS 20 Blood RNA-seq from Prostate cancer patients.

  Raw RNA-seq reads (FASTQ format) and Mapped sequencing reads (BAM format) of 20 Prostate cancer patients in Southern African Prostate Cancer Study (SAPCS). Each patient exhibit different pathogenic variations. The Illumina RNA-sequencing is performed from Blood extraction (from QIAamp RNA Blood Mini Kit). rRNA was removed prior using SortMeRNA. STAR aligner program was used for mapping to human genome GRCh38.p14, resulting in an average genome coverage of 9x.

  Dataset EGAD50000000982

• RNA-Seq data of S24 cells for the publication Recording physiological history of cells with chemical labeling.

  Recordings of elevated calcium levels allowed selections of cells from heterogenous populations for transcriptomic analysis. Paired RNA-Seq from S24 cells using Takara SMARTer Ultra Low Input RNA v4 kit and sequencing on a Illumina NovaSeq 6000.

  Dataset EGAD50000000082

• Molecular profiling of acinar cell carcinoma of the salivary glands

  Samples of acinar cell carcinoma (AciCC) of the salivary glands and paired normal salivary gland tissue were analyzed by whole transcriptome RNA-seq (n=10), whole genome sequencing (n=6), whole genome bisulfite sequencing (n=3) and ChIP-seq (H3K27ac, H3K4me3, H3K27me3, NR4A3, CTCF).

  Study EGAS00001002795

• RNA-seq data of 196 nontumorous human breast tissue

  Transcriptome analysis of nontumorous human breast tissues. 196 cases were included in the dataset.

  Dataset EGAD00001006397

• Transcriptomic hallmarks and RNA isoform diversity in human neurodegenerative disease

  Single-cell RNA-sequencing (scRNA-seq) has enabled high-throughput RNA analysis at an unprecedented resolution. One staple analysis in scRNA-seq is identifying differentially expressed genes (DEGs) between two populations. However, the mRNA isoforms have often been overlooked in these transcriptomic analyses due to technical limitations. In order to investigate the mRNA isoforms at the single-cell level, we used a targeted single-nucleus long-read RNA-sequencing method combining single-nucleus short-read RNA-seq (snRNA-seq), target gene enrichment, and Iso-Seq. We performed snRNA-seq and targeted single-nucleus Iso-Seq (snIso-Seq) on 25 human frontal cortices from individuals with AD, DLB, or PD, and age-matched controls. Our short-read transcriptome analysis revealed that DLB samples had more overlapping DEGs with AD than PD despite sharing pathological hallmarks with PD. We observed vast RNA isoform diversity in the 50 genes targeted, including genes that were not differentially expressed in our short-read data. We also identified several novel isoforms that are not included in the reference annotation. Our data collectively characterize the transcriptome of various neurodegenerative diseases and illuminate the mRNA isoform diversity.

  Study EGAS50000000132

• RNA sequencing of pediatric BCP ALL

  RNA sequencing data of 33 B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) cases were constructed on an Illumina nextseq 2000 Sequencing System.

  Dataset EGAD50000001125

• Uveal melanoma whole genome sequencing, SNP arrays and RNA-seq

  We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

  Dataset EGAD00001000372

• EGAS00001003405 combined RNA, WES, WGS data of 16 gastrointestinal tumor patients

  50 samples of 16 individuals with Gastrointestinal Tumor. Patients were sequenced in various combinations of WGS, Exome and RNA sequencing.

  Dataset EGAD00001005113

• Single cell RNA sequencing of tumor and ascites in high grade ovarian cancer

  Fastq files for single cell RNA sequencing of cells from ovarian cancer tumor and ascites (10X chromium 5' v1.1 libraries). Multiple cases are pooled in each sequencing library.

  Dataset EGAD00001006627

• Transcriptomic analysis of the NA-PHER2 clinical trial

  We performed whole transcriptome RNA sequencing on serial tumour biopsies collected at baseline, Day 14, and after completion of all neoadjuvant therapy from the NA-PHER2 trial. Patients received neoadjuvant treatment with the combined regimen of trastuzumab, pertuzumab, palbociclib with or without addition of fulvestrant. Transcriptomic profiles were generated from 143 samples (Baseline n = 53, Day 14 n = 49, Surgery n = 41) corresponding to 53 of the 58 patients enrolled in NA-PHER2 trial (91.4%). RNA sequencing was performed on total RNA samples derived from formalin-fixed, paraffin-embedded (FFPE) tissue sections. RNA-Seq libraries were produced using NEBNext® Ultra™ II Directional RNA Library Prep Kit. The capture was then performed on cDNA libraries with the Twist Human Core Exome Enrichment System according to supplier recommendations (Twist Bioscience). The obtained eluted-enriched DNA samples was then sequenced on an Illumina NovaSeq as paired-end 100bp reads. FASTQ files are provided.

  Dataset EGAD50000000363

• Histone and transcriptome profiling of glioblastoma initiating cells

  ChIP-seq and RNA-seq of glioblastoma initiating cells and their differentiated counterparts with and without inhibition/knockdown of KDMs.

  Dataset EGAD00001005124

• RNA-seq of chordoma samples

  This dataset contains paired-end bulk RNA-seq data of advanced chordoma samples from 7 patients. Sequencing was performed on Illumina HiSeq 4000 or NovaSeq 6000.

  Dataset EGAD50000001019

• Long-read RNA-seq from 5 patients with stereotyped subset CLL

  Oxford Nanopore Technologies based long-read RNA sequencing data from 5 patients with stereotyped subset CLL. The BAM files were aligned against hg19 reference genome.

  Dataset EGAD50000000755

• RNA-seq dataset of CD34+ HSPCs from LRMDS patients

  To profile transcriptional alterations of HSPCs in LR-MDS patients, 7AAD−CD45+Lin-CD235a−CD34+ cells were isolated from healthy donors and LR-MDS patients for RNA sequencing.

  Dataset EGAD00001015771

• WGS/RNA-seq pair of an inflammatory hepatocellular adenoma (IHCA)

  This study contain the WGS and RNA-seq aligned bam files for this particular inflammatory hepatocellular adenoma sample.

  Dataset EGAD00001004141

• The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

  Dataset contains Exome-seq and RNA-seq from 2 GBM patients, as well as RNA-seq from the derived cultured cells (GNS).

  Dataset EGAD00001001359

• DIPG WES and RNA-Seq

  We characterised H3K27M-mutant diffuse intrinsic pontine glioma (DIPG, n=21) and RNA-Seq (n=26 DIPG, 12 normal brain)

  Dataset EGAD00001006450

• Cancer RNA-seq consisting of FASTQ single-end reads from colon cancer sample

  Cancer RNA-seq consisting of FASTQ single-end reads from 1 colon-cancer individual RNA-seq was performed on illumina This dataset contains reads from a single region.

  Dataset EGAD00001007949

• DAC: Whole transcriptome RNA sequencing as comprehensive diagnostic tool for acute myeloid leukemia.

  Dac EGAC00001000956

• CANCAP03 single-nuclear RNA sequencing

  CANCAP03 single-nuclear RNA sequencing. Tissue punch cores for six patients, 3 from each of olaparib and olaparib and degarelix cohorts, were processed for nuclear isolation and extraction, prior to single-nuclear RNA sequencing. 10x libraries were constructed. Sequencing on NovaSeq 6000. FASTQ files were processed using CellRanger pipeline. Outputs from the CellRanger pipeline were analysed using the Seurat package in R.

  Dataset EGAD50000001280

• DNA sequencing of sgRNAs in CRISPR-Cas9 screening and RNA sequencing of SF3B4-overexpressing liver organoids

  The dataset contains 18 samples. It includs 12 paired whole genome sequencing, and 2 matched short read and long read RNA sequencing of liver organoids, 2 paired RIP RNA sequencing samples. All the experiments were performed on Illumina platform with raw reads stored in fastq format or bam format.

  Dataset EGAD50000001625

• RNA fastq files and mutation annotation files

  This dataset contains the results of both RNA sequencing and DNA sequencing. For RNA sequencing, it includes data from 12 samples derived from 9 patients, provided as raw sequencing files in FASTQ format. For DNA sequencing, it contains mutation information obtained from targeted panel DNA sequencing, including data from 35 individuals in the mutation annotation file (MAF) format.

  Dataset EGAD50000001768

• Single-cell RNA-seq of Bone marrow samples

  For two donors, we collected CD34 plus and CD34 minus hematopoietic cells for the single-cell RNA-seq analysis.

  Dataset EGAD50000000514