7188 results for "({!join from=dataset_studies to=id v=$q1}) OR ("transcriptome" OR "RNA-seq" OR "rna sequencing" OR "rna-sequencing")"

in 148.20 milliseconds.

• Hydroxycarbamide effect on gene expression in MPN

  Whole RNA-sequencing of CD34+ cells and neutrophils derived from MPN patients before hydroxycarbamide treatment and after 9-months of treatment. CD34+ cells= 5 patients, 10 samples; neutrophils= 7 patients, 14 samples. Fastq files provided.

  Dataset EGAD00001006330

• Results of single-cell sequencing of adipose-derived mesenchymal stromal cells and dermal fibroblasts.

  Adipose-derived mesenchymal stromal cells from subcutaneous (n=4) and visceral (n=4) tissue, along with dermal fibroblasts (n=3) were analyzed by single-cell RNA sequencing.

  Dataset EGAD00001009995

• Patient-derived GBM cultures TMZ+BMP4 treated

  Batch RNA sequencing of passages 5-7 of three patient-derived monolayer glioblastoma cultures in which TMZ and BMP4 synergize. 3 biological replicates, either untreated, only temozolomide, only BMP4 or temozolomide + BMP4

  Dataset EGAD00001010163

• Single cell RNA sequencing of colorectal cancer patients (KUL3)

  All libraries were sequenced on Illumina HiSeq4000 until sufficient saturation was reached.

  Dataset EGAD00001008584

• Dataset for ARHGAP11A knockout and control organoid cells.

  This dataset contains 9 RNA sequencing samples of hiPSC-derived forebrain organoid ARHGAP11A knockout and hiPSC-derived forebrain organoid control cells. Sequencing was performed on Illumina NovaSeq 6000. The sequencing was always paired.

  Dataset EGAD00001015706

• 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

• PRADO trial - Personalized response-directed surgery and adjuvant therapy after neoadjuvant ipilimumab plus nivolumab in stage III melanoma

  The dataset includes RNA sequencing data on PRE- treatment biopsies of lymph node metastasis (n=80) The technology used for sequencing is llumina HiSeq 2500

  Dataset EGAD00001012116

• RNA data of neuroblastoma patients

  94 sample with multi-omics analysis of ALT-positive neuroblastoma tumors, rna sequencing

  Dataset EGAD00001006587

• Smart-seq2 raw reads of human kidney glomerular single cells

  Smart-seq2 single cell RNA sequencing reads from kidney glomerular single cells of healthy human individuals. The dataset contains single-end fastq files of 766 single cells.

  Dataset EGAD00001006861

• Microvascular Permeability, Inflammation, and Lesion Physiology in Endometriosis: A Microphysiological Systems Approach

  The goal of the study is to identify novel molecular pathways involved in the etiology of endometriosis and to develop in vitro model systems to enable the study of the mechanisms regulating reproductive function. Using a physiomimetic modeling approach, primary tissue samples of the human endometrium derived from patients diagnosed with and without endometriosis and/or endometriotic diseases (e.g. adenomyosis) were used for secondary analysis using multi-omic systems biology analysis and to build tissue engineered models. We performed single cell RNA sequencing (scRNA-Seq, N=6)) to study the cellular and transcriptomic composition of the endometrial tissue microenvironment and proteomics (LC-MS/MS) to study protein-level signaling pathways and the matrisome of the native endometrium. Systems biology analysis of these datasets helped identified a putative dysregulated inflammatory signaling pathway in endometriosis patients compared to controls. Moreover, subsets from these scRNA-Seq and proteomic datasets were used to aid the design of a synthetic extracellular matrix hydrogel as an in vitro platform for the culture of endometrial cells. Tissue-engineered synthetic PEG hydrogel enables the simultaneous co-culture of endometrial epithelial organoids and stromal fibroblasts in a fully defined, 3D, and tunable environment. We demonstrated that the in vitro co-culture model recapitulates key phenotypic processes observed across the human menstrual cycle in response to sex hormone stimulation through both biochemical and transcriptomic (bulk RNA-sequencing) analysis. This model will enable future mechanistic studies that examine origins of endometriotic disease phenotypes. The transcriptomic data generated for this study including the scRNA-Seq data from primary human endometrial tissues and the bulk RNA-Seq datasets from the experimental co-culture models is available through dbGAP.

  Study phs003326

• STAR outputs from RNA-seq

  STAR outputs from RNA-seq of 84 pancreatic neuroendocrine neoplasms, 10 normal islet samples and 4 cell line samples.

  Dataset EGAD00001006991

• Intellance-2: TruSight Tumor 170 panel based RNA-seq

  Intellance-2: TruSight Tumor 170 panel based RNA-seq

  Dataset EGAD00001007944

• RNA-Seq of pancreatic neuroendocrine tumors mutated in MEN1/DAXX/ ATRX

  RNA-Seq of of 11 primary pancreatic neuroendocrine tumors mutated in MEN1/DAXX/ ATRX used to identify molecular subtypes

  Dataset EGAD00001015695

• Smart-seq2 single-cell RNA-seq of human liver non-parenchymal cells

  Smart-seq2 single-cell RNA-seq of human liver non-parenchymal cells from lean and obese individuals

  Dataset EGAD00001010301

• RNA-Seq datasets in human islets cultured in low glucose conditions

  7 RNA-Seq datasets in human pancreatic islets from 7 donors, where islets were using low (4mM) glucose conditions.

  Dataset EGAD00001005208

• Human tumour bulk RNA-seq

  We profiled 18 high-grade gliomas patient tumor samples by bulk RNA-seq. The raw fastqs are provided.

  Dataset EGAD00001006098

• RNA-Seq of serially passaged TIC-enriched spheres of colorectal cancer

  18 samples of RNA-Seq of serially passaged TIC-enriched spheres of colorectal cancer (CRC), sequenced on HiSeq2000 and HiSeq2500

  Dataset EGAD00001006264

• RNA-SEQ for the Caldas Lab breast cancer PDTX collection

  RNA-SEQ for the Caldas Lab breast cancer PDTX collection. This includes both single and paired end runs

  Dataset EGAD00001006307

• Prostate Cancer - RNA-Seq unmapped reads

  Prostate Cancer - RNA-Seq unmapped reads

  Dataset EGAD00001003756

• Analysis of Treg gene expression patterns by RNA-Seq in patients with rheumatoid arthritis (RA) and healthy controls (HCs) : Comparison between young and elderly individuals

  We compared the gene expression of CD4+CD45RA-CD25hiCD127lo Treg cells from PBMCs between young and elderly RA patients and HCs by RNA-seq

  Study JGAS000693

• NGS-ProToCol prostate cancer RNA-seq data.

  NGS-ProToCol RNA-seq dataset contains 41x normal adjacent prostate and 51x prostate cancer samples taken from fresh frozen radical prostatectomies, sequenced using random-hexamer priming. RNA-seq was performed on the Illumina HiSeq 2500 platform, 2 x 126 bp stranded paired-end reads at a depth of 70 mln reads.

  Dataset EGAD00001004215

• RNA-seq data from hypothalamic tissue from individuals with Prader-Willi syndrome and age-matched controls.

  RNA-seq data (bam files) from the hypothalamus of 4 individuals with Prader-Willi syndrome and 4 age-matched control individuals. Detailed information about the study design, case-control matching and RNA-seq data processing is provided in the accompanying publication [Bochukova et al (2018) Cell Reports].

  Dataset EGAD00001004034

• Study of Leukemia Stem Cells in B-ALL

  This study focused on the biologic properties of human B acute lymphoblastic leukemia (ALL) stem cells. We used human leukemia cell lines, primary patient specimens, and patient derived xenografts in experiments using ChIP-seq, bulk RNA sequencing, single cell RNA sequencing, and CITE-seq.

  Study phs002492

• Transcriptome sequencing of cancer cell lines

  This dataset contains RNA sequencing data for 675 cancer cell lines. RNA libraries were made with the TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer protocol. The libraries were sequenced on an Illumnia HiSeq 2000

  Dataset EGAD00001000725

• Circulating RNAs prior to endometrial cancer diagnosis

  We analyzed circulating RNA levels using small RNA sequencing, targeting RNA in the size range 17 to 47 nucleotides, in samples collected prior to endometrial cancer diagnosis compared to cancer-free controls. The analysis included 316 cases with samples collected 1-11 years prior to diagnosis , and 316 matched controls, both from the Janus Serum Bank Cohort in Norway.

  Study EGAS50000000267

• Single cell atlas of large B-cell lymphoma

  The dataset comprises multi-omics profiles from 232 biopsies, including 217 from patients with large B-cell lymphoma (114 newly diagnosed and 103 relapsed/refractory) and 15 benign control samples. Specifically: single-nucleus RNA sequencing (snRNA-seq) was performed on all 232 biopsies; single-nucleus ATAC sequencing was conducted on 96 biopsies; bulk RNA sequencing was generated for 208 biopsies; whole-exome sequencing (WES) was performed on 174 tumor biopsies with 118 matched germline samples; Low-pass whole-genome sequencing (lpWGS) was performed on 174 tumor biopsies with 41 matched germline samples. All raw data files are provided in FASTQ format.

  Dataset EGAD50000001491

• Spatial transcriptome analysis of aging of healthy skin samples

  Previous studies have revealed that skin T cells accumulate and maintain immune responses in the elderly. However, we questioned why these functional T cells fail to recognize and eliminate malignant cells, making elderly skin more prone to developing malignant tumors. To address this question, we examined the overall skin microenvironment in aging using Xenium digital spatial RNA sequencing.

  Study JGAS000771

• Whole-genome and transcriptome sequencing of primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma

  Primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma (pcAECyTCL) is a rare variant of cutaneous T-cell lymphoma with an aggressive clinical course and a very poor prognosis. We subjected tumor biopsies from patients with pcAECyTCL to whole-genome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

  Study EGAS00001004332

• Single cell RNA sequencing data in "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2"

  This dataset includes a total of 5 single cell RNA sequencing (scRNAseq) data of SARS-CoV-2 infected human alveolar stem cell culture models. Two scRNAseq data were obtained from SARS-CoV-2 infection with MOI of 1.0 (1 for control and 1 for infected case) and the other three were obtained from SARS-CoV-2 infection with MOI of 0.1 in the study entitled "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2". The 10x Chromium Single Cell 3' Reagent kits were used to generate libraries.

  Dataset EGAD00001006242

• Whole genome and RNA-sequencing in T-cell acute lymphoblastic leukemia

  Dataset includes whole genome and transcriptomic sequencing data from five T-cell acute lymphoblastic leukemia (T-ALL) patients. Whole genome sequencing has performed from both diagnostic (T-ALL sample) and control (remission sample) samples. RNA-sequencing has performed from diagnostic samples. Samples has been taken from the bone marrow or peripheral blood.

  Dataset EGAD00001008658

• Single-cell RNA sequencing of breast cancer lung metastasis and adjacent normal tissue

  This dataset contains single-cell RNA sequencing data from two samples: L1 (breast cancer metastasis to lung) and N3 (adjacent normal lung tissue) from a female patient. The samples were processed using 10X Chromium 3' technology and sequenced on Illumina NextSeq 500. This data supports the study "Endocrine therapy reprogramming of breast cancer facilitates metastatic escape via upregulation of P-Rex1/Rac1 signalling" which investigates how endocrine therapy reprograms breast cancer cells, leading to upregulation of P-Rex1/Rac1 signalling pathways that facilitate metastatic escape. The single-cell analysis reveals cellular reprogramming mechanisms in endocrine therapy-resistant breast cancer cells that form metastases in the lung.

  Dataset EGAD00001015769

• Transcriptomic profiling of RIRCD patient skeletal muscle, comparing muscle during affected phase to healthy control, and affected patient with and without additional EARS2 mutations.

  Illumina Nextseq total RNA sequencing profiles of skeletal muscle biopsies of 5 affected patients (F3/2M, F4/1F, F5/1M, F2/2F, F2/1M) compared to 6 control (Control040500, Control3509, Control3934, Control3949, Control4994, Control5106) and comparing 3 patients with additional EARS2 mutations (F2/2F, F2/1M, F5/1M) to 2 patients without (F3/2M, F4/1F). Illumina MiSeq total RNA sequencing profiles of skeletal muscle biopsies from patient F3/1M during affected disease phase (4 replicates: F3-1M_Affected_1, F3-1M_Affected_2, F3-1M_Affected_3, F3-1M_Affected_4) compared to recovered phase (F3-1M_Recovered_1, F3-1M_Recovered_2, F3-1M_Recovered_3, F3-1M_Recovered_4).

  Dataset EGAD00001006381

• Bulk RNA sequencing of hematological toxicity following CAR-T cells injection

  Bone marrow aspirations obtained from patients treated with CAR-T cells were analyzed using bulk RNA sequencing (CD3+, CAR T+, CD34+ sorted populations).

  Study EGAS50000000777

• Single-cell RNA-sequencing for peripheral blood mononuclear cells from COVID-19 patients and healthy controls of Japanese

  We performed single-cell RNA-sequencing of peripheral blood mononuclear cells obtained from COVID-19 patients and healthy controls.

  Study JGAS000593

• Single-cell RNA-sequencing for peripheral blood mononuclear cells from COVID-19 patients and healthy controls of Japanese

  We performed single-cell RNA-sequencing of peripheral blood mononuclear cells obtained from COVID-19 patients and healthy controls.

  Study JGAS000543

• Single cell RNA-sequencing of GSCs and GBM tumours

  Characterization of glioblastoma tumors and glioblastoma stem cell (GSCs) lines with single cell or single nuclei RNA-sequencing.

  Study EGAS00001004656

• RNA-sequencing of Non-muscle Invasive Bladder cancer (NMIBC)

  This RNA-sequencing cohort includes 78 Non-muscle Invasive Bladder cancer (NMIBC) samples and 7 Muscle Invasive Bladder cancer (MIBC) samples.

  Study EGAS00001004358

• RNA sequencing of AD, MCI and control OM cells

  Total RNA sequencing of cultured OM cells derived from patients with Alzheimer's disease (AD), individuals with mild cognitive impairment (MCI) and cognitively healthy controls.

  Study EGAS00001006195

• Paired-end RNA-seq analysis of the TERT promoter mutant GBM cell lines

  This dataset contains 9 RNA-seq BAM files. RNA was derived from TERT promoter mutant GBM cell lines and sequenced on an Illumina HiSeq4000 sequencer with paired-end reads and an average read length of 50 base pairs. Reads were aligned with TopHat (v2.0.14) using a GENCODE V19 transcriptome-guided alignment.

  Dataset EGAD00001005435

• RNA-seq

  Bulk RNA-seq data of 8 RNA samples were generated. Libraries were prepared using the Stranded mRNA Library Prep, Ligation Kit (Illumina) following manufacturer’s recommendations and sequenced on a NextSeq 2000 (2x50 bp, Illumina).

  Dataset EGAD00001010308

• PCa-LINES: rRNA-minus RNA-seq of PCa cell-lines (VCaP & PC346c) and 5 additional patient samples

  PCa-LINES: rRNA-minus RNA-seq of PCa cell-lines (VCaP & PC346c) and 4 additional patient samples

  Dataset EGAD00001006366

• Human normal brain bulk RNA-seq

  We profiled 43 normal human adult brain and 11 normal human fetal brain specimens by bulk RNA-seq. The raw fastqs are provided.

  Dataset EGAD00001005130

• RNA-Seq datasets in human islets cultured in high glucose conditions

  7 RNA-Seq datasets in human pancreatic islets from 7 donors, where islets were treated in high (11mM) glucose conditions

  Dataset EGAD00001005207

• Human tumor bulk RNA-seq

  We profiled 7 patient neuroblastoma-FOXR2 tumor samples by bulk RNA-seq. The raw fastqs are provided.

  Dataset EGAD00001010901

• Human Pancreatic Beta Cell lncRNAs Control Cell-Specific Regulatory Networks - Whole Human Islet paired-ended RNA-seq assays

  Whole Human Islet paired-ended RNA-seq of 64 human pancreatic donors.

  Dataset EGAD00001003992

• 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

• Gastric cancer RNA-seq data

  strand-specific RNA-seq data from 19 gastric tumors and their adjacent normal tissues, plus 16 gastric cancer cell lines, one normal gastric cell line, and 3 normal stomach RNAs

  Dataset EGAD00001003448

• Prostate Cancer - RNA-Seq unmapped reads

  Prostate Cancer - RNA-Seq unmapped reads

  Dataset EGAD00001004424

• RNA-seq data from 195 pediatric BCP-ALL cases

  RNA-seq data from 195 pediatric BCP-ALL cases. Alignment: TopHat 2.0.7. Reference genome: hg19.

  Dataset EGAD00001002112

• Landscape of somatic mutations and DNA copy number alterations and transcriptomic profiling identifies metabolic reprogramming as a hallmark of ibrutinib resistance

  Whole-exome sequencing (WES) was conducted on the clinical specimens of 14 cases that had sufficient isolated tumor DNA, including 7 ibrutinib-sensitive cases and 7 ibrutinib-resistant cases. Whole transcriptome sequencing (RNA-seq) was performed on clinical specimens isolated from 14 ibrutinib-sensitive and 7 ibrutinib-resistant cases. Unsupervised hierarchical clustering of MCL tumors using RNA-seq gene expression data showed a response-specific gene expression signature.

  Study EGAS00001003418