9296 results for "cancer rna-seq"

in 73.67 milliseconds.

• Recurrent Somatic Mutations in CLL

  Study EGAS00001000070

• Genetic alterations in metastatic uveal melanoma

  Study EGAS00001003303

• OSCC WES + WGS Boot et al. 2020

  Study EGAS00001004376

• "Data Access Center Cancer Genomics Group"

  Dac EGAC00001000030

• DAC for the Prostate Cancer Lymph Node dataset

  Dac EGAC00001000586

• The Ovarian Cancer Association Consortium Data Access Committee

  Dac EGAC00001000616

• THE NOWAC BLOOD-BREAST CANCER COMMITEE DATA ACCESS AGREEMENT

  Dac EGAC00001000743

• DAC for study Non-coding RNAs in Breast Cancer

  Dac EGAC00001001090

• Children's Cancer Therapy Development Institute Data Access Commitee

  Dac EGAC00001001160

• DAC for GAMuT Project - Peter MacCallum Cancer Centre

  Dac EGAC00001001278

• DAC for Angiosarcoma Study. National Cancer Centre Singapore.

  Dac EGAC00001001311

• ASAN Center for Cancer Genome Discovery Data Access Commitee

  Dac EGAC00001001391

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001001404

• Hereditary Cancer Diagnostics with I2HCP Data Access Comitee

  Dac EGAC00001001541

• Inherited Predisposition to Cancer Projects Data Access Committee

  Dac EGAC00001001565

• Immunogenomics of Colorectal Cancer Data Access Committee

  Dac EGAC00001001596

• UZ Ghent Prostate Cancer Team Data Access Committee

  Dac EGAC00001001608

• Cancer Alliance Data Access Committee

  Dac EGAC00001001641

• Primary tumor and metastatic breast cancer data access

  Dac EGAC00001001687

• Breast Cancer Single-Cell Data Access Committee

  Dac EGAC00001001974

• Data access committee breast cancer whole genome sequencing HRD

  Dac EGAC00001002286

• Leeds institute of Medical Research Bladder Cancer Research Group

  Dac EGAC00001002397

• MSKCC Colorectal Cancer Plasma WGS Data Access Comittee

  Dac EGAC00001002741

• Southern African Prostate Cancer Study (SAPCS) Data Access Committee

  Dac EGAC00001002768

• Netherlands Cancer Institute (NKI) - Beatriz Carvalho group

  Dac EGAC00001003134

• Cancer Team Data Access Committee

  Dac EGAC00001003407

• FunGeST - Functional Genomics from cancer research to personalized medicine

  Dac EGAC00001002924

• Paired healthy & tumor organoid Biobank _B15PON

  Study EGAS00001005865

• NOWAC blood-breast cancer Data Access Committee

  Dac EGAC01000000024

• PD-L1 blockade immunotherapy rewires cancer-induced emergency myelopoiesis

  Dac EGAC00001003503

• Aberrant EZHIP Expression Drives Tumorigenesis in Osteosarcoma

  Study EGAS00001007531

• Berlin Neuroblastoma Dataset

  Study EGAS00001004022

• Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm and the mitochondrial double membrane. Despite these physical barriers we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements and the features of the fusion fragments indicate that non-homologous end joining and/or replication-dependent DNA double strand break repair are the dominant mechanism involved. This study includes 12 pairs of whole-genome sequences (tumour and paired-normal), which present somatic mitochondrial DNA integrations in tumour genomes. Reference: Young Seok Ju et al., Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells, Genome Research (2015).

  Study EGAS00001001234

• A benchmarking resource for NGS testing of cancer predisposition genes

  A benchmarking resource of 639 individuals, to assess the analytical sensitivity of cancer predisposition gene (CPG) testing.The dataset includes sequencing data generated using the TruSight Cancer Panel (TSCP) a targeted NGS assay for analysis of CPGs and orthogonally generated data supporting at least one pathogenic variant in a CPG for a total of 645 pathogenic CPG variants.The set of pathogenic CPG variants includes strong representation of some of the most challenging types of pathogenic variants, with 339 indels, including 16 complex indels and 24 insertions or deletions with length greater than 5bp, and 74 exon CNVs, including 23 single exon CNVs. There are 502 pathogenic variants in BRCA1 or BRCA2, making this an important first-line validation dataset for laboratories performing NGS testing of BRCA1 and BRCA2.

  Study EGAS00001002993

• Comprehensive Molecular Analysis of Colon Cancer for the Identification and Validation of New Biomarkers

  This study aims to identify diagnostic and prognostic biomarkers in colon cancer and to study understand the complex genomic, genetic and epigenetic relationships with a multiomic approach. The study includes tumor and paired normal mucosa of 100 colon cancer patients diagnosed at stage II, untreated and with microsatellite stable tumours. Also 50 normal mucosa samples from healthy donors are included as reference. The samples have been analysed for gene expression with Affymetrix U219 array (available at GEO GSE44076), SNP/CNV with the Affymetrix 6.0 Human SNP array, for DNA methylation with the Illumina 450K array. Small RNAs were sequenced with the Solid technology and 42 of the tumours and paired normal mucosa DNA were whole exome sequenced with Illumina Genome Analyzer.

  Study EGAS00001002453

• Longitudinal monitoring of cell-free DNA methylation in ALK-positive non-small cell lung cancer patients

  Here, we performed genome-wide 5-mC profiling in plasma of metastatic ALK-rearranged non-small cell lung cancer (NSCLC) patients receiving tyrosine kinase inhibitor therapy. We established a strategy to identify ALK-specific 5-mC changes from cfDNA and demonstrated the suitability of the identified markers for cancer detection, prognosis and therapy monitoring. Longitudinal plasma samples (n = 79) of 21 ALK-positive NSCLC patients and 13 healthy donors were collected alongside 15 ALK-positive tumor tissue and 10 healthy lung tissue specimens. All plasma and tissue samples were analyzed by cell-free DNA methylation immunoprecipitation sequencing to generate genome-wide 5-mC profiles. Information on genomic alterations (i.e., somatic mutations/fusions and copy number alterations) determined in matched plasma samples were available from previous studies.

  Study EGAS00001006573

• Clinical Cancer Sequencing

  Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES from formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output similar to data from frozen samples, and (3) clinical interpretation of WES data for prospective use. In this study, we describe a prospective clinical WES platform for archival FFPE tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a "long tail" of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. Overall, this methodology may inform the widespread implementation of precision cancer medicine.

  Study phs000694

• Evolution of Resistance in ER+ Breast Cancer

  While the combination of endocrine therapy and CDK4/CDK6 inhibitors has been shown to be effective in the metastatic ER+ breast cancer setting, to test whether it is effective in an earlier stage neoadjuvant setting, the FELINE trial (NCT02712723) was established to test the efficacy of letrozole and ribociclib in a ER-positive, HER2-negative patients in a randomized, placebo-controlled, multicenter trial. Patients were randomized to one of three arms: those in Arm A received letrozole and placebo, Arm B letrozole and intermittent ribociclib, and Arm C letrozole and continuous ribociclib. Samples were collected at screening (Day 0), Cycle 1 (Day 14), and end of trial (Day 180). Samples from 24 patients, where cancer cells were present at Day 0 and one additional time point, were subjected to whole-exome sequencing profiling.

  Study phs002287

• TCGA WGS Variants Across 18 Cancer Types

  Even though whole genome sequence (WGS) data has been generated and published in many studies, much of this information is not yet processed for use in down-stream analysis. This study's aim is to provide 1342 WGS normal-tumor paired single nucleotide variations (SNP) over 18 different cancer types provided by The Cancer Genome Atlas (TCGA) project. Individual level data for TCGA can be accessed by requesting access for phs000178. This data includes variations within self-reported white and African-American populations. Variations that exist within the tumor tissue but are absent in associated normal organ tissue (as compared to the human reference genome) are reported. Data published includes SNP and small insertions and deletions, which were generated through a pipeline including the VarScan2 variant calling software.

  Study phs003155

• Renal Cancer Exome Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Dataset EGAD00001000014

• Renal Cancer Exome Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Dataset EGAD00001000287

• Lung Plasma rearrangement screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Dataset EGAD00001000367

• PLCRC study

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from Colorectal cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Dataset EGAD00001000947

• Targeted Pulldown Validation of mutations found in whole genome sequencing

  This experiment is to inform us of the validity of using pre-made library material to perform a bespoke pulldown experiment to validate the mutations found between the whole genome sequencing of the DNA from the same individuals cancer and normal material. This is to identify the valid and informative mutations in cancer genomes.

  Dataset EGAD00001001061

• CNV detection in targeted NGS panel data

  We present targeted NGS panel data from 170 samples that were processed using the TruSightTM Cancer (TSC) panel (Illumina, San Diego, CA, USA), which targets 94 genes and 284 SNPs associated with a predisposition towards cancer. The samples are enriched for CNVs in the genes of interest. All CNVs have previously been assessed with MLPA and can therefore be considered as confirmed.

  Dataset EGAD00001003400

• Colorectal cancer WES/WGS analysis in Dr. Liu’s group in Sun Yat-sen University Cancer Center

  The samples include paired tumor and normal tissues from 205 patients (201 for normal and primary tumor tissues; 4 for normal, primary tumor and liver metastatic tissues). High-coverage WES sequencing or whole genome sequencing of DNA samples were performed on the Illumina HiSeq 2000 system

  Dataset EGAD00001003452

• Whole Exome sequencing of Gingivo-buccal Cancer - ICGC India Project Batch04

  This dataset pertains to whole exome sequencing of paired DNA samples of Gingivo-buccal oral cancer patient.DNA was isolated from the tumor and blood tissues of 47 patients (94 samples).We have performed Nextera exome capture and sequenced exome libraries in Illumina HiSeq platform.We have uploaded BWA-ALN aligned BAM files.

  Dataset EGAD00001003987

• Whole exome profiling of spatial biopsies of high grade serous epithelial ovarian cancer patients

  This data set is comprised of data from seven distinct high grade serous epithelial ovarian cancer (HGS-EOC) partients, from whom multiple biopsies were taken at the time of surgery, from the ovary and from different locations in the peritoneal cavity. This data set contains 28 samples, sequenced with a whole exome sequencing approach.

  Dataset EGAD00001004154

• Shallow whole genome sequencing on stage 1 epithelial ovarian cancer

  BAM files (aligned against the hg38 genome) from a shallow whole-genome sequencing experiment (median depth 0.5X) on 218 samples from Stage 1 epithelial ovarian cancer biopises. Samples labeled "bis" or "tris" with the same ID are relapses; "left" or "right" samples indicate, in the case of bilateral tumor, from which ovary the sample was taken.

  Dataset EGAD00001006881

• Whole genome shotgun sequencing and somatic mutations data in Hepatocellular carcinoma

  Hepatocellular carcinoma (HCC) is the most common malignancy of the liver. Genomic analysis is conducted to identify genetic alterations in driver genes which are all druggable targets for cancer therapy.

  Study EGAS00001002578

• Sequencing of longitudinal glioma pairs

  Clonal evolution drives cancer progression and therapeutic resistance. Recent studies revealed divergent longitudinal trajectories in gliomas, but early molecular traits steering post-treatment cancer evolution remain unclear. We analyzed sequencing data of 544 initial-recurrent adult diffuse glioma pairs to identify genomic and transcriptomic early predictors of tumor evolution in each molecular subtype.

  Dataset EGAD00001009845

• Comprehensive analyses of clinicopathological features and genomic mutations of combined hepatocellular-cholangiocarcinoma

  Combined hepatocellular and cholangiocarcinoma (cHCC-CCA) is a rare primary liver cancer. We performed whole exome sequencing to clarify the relationship between genetic mutations and clinicopathological features in cHCC-CCA.

  Study JGAS000599

• Illumina TSO500 DNA Dataset for Manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Illumina TSO500 DNA Dataset for Manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Dataset EGAD00001015396

• Optimized Polyepitope Neoantigen DNA Vaccines Elicit Neoantigen-Specific Immune Responses in Preclinical Models and in Clinical Translation

  A patient with Lynch syndrome and a neuroendocrine tumor sequenced with exome, whole genome, and bulk RNAseq. Sequence data was used to create a personalized cancer vaccine.

  Study phs002342

• H3K27ac ChIP-seq in primary inflammatory macrophages from 2 minor allele homozygotes and 2 major allele homozygotes at rs2836882

  This dataset consists of H3K27ac ChIP-sequencing in inflammatory (TPP) macrophages from 2 minor allele homozygotes and 2 major allele homozygotes at rs2836882. Monocytes were positively selected from PBMC using CD14 Microbeads and inflammatory macrophage differentiation performed using conditions that model chronic inflammation (TPP): 3 days GM-CSF (50ng/mL) followed by 3 days GM-CSF, TNFa (50ng/mL), PGE2 (1mg/mL), and Pam3CSK4 (1mg/mL). After harvesting, cells were cross-linked, quenched, lysed, and sheared. Immunoprecipitation of histone-DNA complexes was performed overnight at 4C with rotation using an anti-H3K27ac antibody and the SimpleChIP Plus Sonication ChIP kit (Cell Signaling Technology). Following reverse cross-linking, 50ng of immunoprecipitated DNA or input DNA were used to prepare sequencing libraries using the iDeal Library Preparation kit (Diagenode), according to manufacturer instructions. 10 PCR cycles were used for the amplification step and size selection was not performed. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 (Agilent) and the libraries were sequenced in pools of 8, with each pool being sequenced in 2 lanes of an Illumina HiSeq2500 high output flow-cell (50bp, single-end reads). Raw data are provided as raw and aligned single-end sequencing reads from H3K27ac-bound DNA and the input chromatin. Raw reads were trimmed using Trim Galore and aligned to the reference human genome (hg19) using Burrows-Wheeler Aligner (v0.7.12) with default parameters. Aligned reads were converted to BAM files, sorted, and technical duplicates merged before indexing – all using SAMtools (v1.4). PCR duplicates were identified using Picard tools (v2.18.1) and removed together with unmapped reads using SAMtools (v1.4). The resulting BAM files were re-sorted and indexed after filtering.

  Dataset EGAD00001011351

• The PEACE (Posthumous Evaluation of Advanced Cancer Environment) Study DAC

  Dac EGAC00001003055

• Primary breast tumor heterogeneity through therapy

  Study EGAS00001003168

• DAC for integrated genomics of metastatic prostate cancer

  Dac EGAC00001000230

• JAK and STAT alterations in CD30 positive LPD

  Study EGAS00001004181

• Genomic and transcriptome analysis for intrahepatic cholangiocarcinoma

  Study EGAS00001006007

• The NOWAC blood-breast cancer commitee data access agreement

  Dac EGAC00001000684

• Breast cancer multi-region sequencing from Sottoriva Lab

  Dac EGAC00001000890

• Harbin Medical University Cancer Hospital Data Access Commitee

  Dac EGAC00001000948

• UT MD Anderson Cancer Center Genomic Medicine and Leukemia

  Dac EGAC00001001252

• ASAN Center for Cancer Genome Discovery Data Access Commitee

  Dac EGAC00001001285

• Cancer Sequencing Data Access Committee

  Dac EGAC00001001428

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001001505

• The data usage policy for epigenomic profile of diverse cancer

  Dac EGAC00001001540

• INSERM U981 Team : Genomics of Non-Melanoma Skin Cancer

  Dac EGAC00001001644

• Princess Margaret Head and Neck Cancer Data Access Committee

  Dac EGAC00001001647

• Zero Childhood Cancer

  Dac EGAC00001001683

• Imperial College Tumour Immunology group - Surgery and Cancer DAC

  Dac EGAC00001001814

• Division of Cellular Signaling National Cancer Center Research Institute

  Dac EGAC00001001909

• Whole Exome Sequencing of Mixed Histology Lung Cancer at MDACC

  Dac EGAC00001002034

• MRC Institute of Genetics and Cancer Data Access Committee

  Dac EGAC00001002163

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001002510

• Hoag Family Cancer Institute Carcinoid Multiomic Study Data Access Committee

  Dac EGAC00001003084

• TCR sequencing of TIL in breast cancer data access committee

  Dac EGAC00001003173

• DAC - The Netherlands Cancer Institute - Antoni van Leeuwenhoek

  Dac EGAC00001003316

• Common and rare germline variants in Japanese prostate cancer patients

  Study JGAS000487

• Single Cell RNAseq of PBMC from renal cancer patients

  Dac EGAC00001001605

• Human primary and metastatic colorectal cancer (CRC) samples

  Study EGAS00001006746

• Targeted sequence of MDS cases treated with azacitidine

  Study EGAS00001007030

• BRCA-deficiency/HRD in individuals with HBOC

  Study EGAS00001007258

• Berlin Neuroblastoma Dataset Update 2021

  Study EGAS00001005604

• Gtag&T single-cell genome and transcriptome data

  Study EGAS00001007043

• Expression quantitative trait locus mapping in human pancreatic islets of Langerhans

  The intersection of genome-wide association analyses with physiological and functional data indicates that variants regulating islet gene transcription influence type 2 diabetes (T2D) predisposition and glucose homeostasis. However, the specific genes through which these regulatory variants act remain poorly characterized. To identify such effector transcripts for T2D and glycemic traits, we generated expression quantitative trait locus (eQTL) data in 118 human islet samples using RNA-sequencing and high-density genotyping.

  Dataset EGAD00001001601

• DCM-cases

  DCM-cases (149 human DCM samples) human heart biopsies from 149 patients with dilated cardiomyopathy (DCM) were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls.

  Dataset EGAD00001003390

• ETMR_Nanostring

  Total RNA (100ng) from 21 ETMRs with C19MC structural alterations and 28 other PBTs was prepared with nCounter miRNA Sample Prep Kit according to standard protocol. miRNA expression profiling was conducted with human v1, v2, or v3 miRNA panel on nCounter miRNA expression platform (NanoString Technologies, Seattle, WA) according to manufacturer’s protocol. Signal normalization was done using nSolver Analysis and batch corrected using ComBat (Johnson et al. Biostatistics. 2007). 565 miRNAs overlapped between all three versions and was used for further analyses. Fold change and supervised t-test with FDR correction was calculated between the ETMRs and other PBTs.

  Dataset EGAD00010001701

• PIVUS study - Longitudinal transcriptomics - Advanced aging

  We performed RNA sequencing in whole-blood from the same 65 individuals from the PIVUS study at ages 70 and 80 (130 samples) to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging. Each individual has four fastq files, two for each age. Consecutive sample IDs refer to the sample individual, e.g. PIVUS003 and PIVUS004 are the age 70 and age 80 samples of the first individual.

  Dataset EGAD00001004965

• Targeted gene panel sequencing of matched diagnosis-remission-relapse B cell precursor acute lymphoblastic leukemia samples

  Bone marrow mononuclear cells from patients diagnosed with B cell precursor acute lymphoblastic leukemia were obtained at three sequential time points: first diagnosis, remission after chemotherapy and relapse. Genomic DNA was isolated and targeted gene panel sequencing was performed using a customized biotinylated RNA oligo pool (SureSelect, Agilent, Santa Clara, California) to hybridize the target regions comprising 362 kbp on a HiSeq2000. Target regions were selected to validate mutations previously identified in these samples using whole exome sequencing.

  Dataset EGAD00001004977

• Mapping genetic variants underlying gene regulation in healthy intestinal cell types to identify novel IBD drug targets (2020-05-12)

  Biopsies from the terminal ileum and rectum of healthy individuals are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-05-12.

  Dataset EGAD00001006139

• Processed microarray gene expression data from NPC samples_Cohort 2

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006274

• Processed microarray gene expression data from NPC samples_Cohort 1

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006275

• Detection of Gene Fusions using Targeted Next-Generation Sequencing

  Five commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).

  Dataset EGAD00001006913

• single cell RNA sequencing of resting and IAV-stimulated mononuclear phagocytes of Africans and Europeans

  CD14+ monocytes from 4 African and 4 Europeans individuals with varying degree of ex-vivo susceptibility to Influenza, were either stimulated with Influenza A virus, or left resting. Cells from all 16 samples were collected at 4 time points (0, 2, 4, 6h post infection), and pooled across 13 libraries. Samples were processed on the 10x chromium with 3' reagents kits, V3 chemistry and sequenced with Hiseq X ten.

  Dataset EGAD00001006938

• Patient-derived gene and protein expression signatures of NGLY1 deficiency

  Single-end bulk RNA sequencing results of cell lines derived from patients described with NGLY1 deficiency as well as parent and CRISPR edited controls. The cell lines represent 4 different cell types: fibroblasts, lymphoblastoid cells, induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs.).

  Dataset EGAD00001008094

• Single-cell GoT sequencing from CH, MDS and AML patients with CH mutations

  Single-cell targeted amplicon RNA sequencing from CH (n = 3), MDS (n = 6, MDS02 in 2 replicates) and AML (n =1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8 [2 -CH, 6 MDS], U2AF1 n = 1) or transcription regulators (DNMT3A - CH04). The transcripts are targeted to detect a particular CH mutation in the listed genes. U2AF1 GoT are full-length cDNA, while the rest follow the 10x 3' V3 protocol.

  Dataset EGAD00001011284

• Next Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Human Systemic Lupus Eryhtematosus (2)

  This dataset contains RNA-sequencing of Bone marrow-derived CD34+ cells from Healthy Controls (n=2) and SLE patients (n=10). SLE patients are divided into two categories based on severity: patients with moderate/mild disease (n=4) and patients with severe disease (n=6). Libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500. The raw fastq files are uploaded.

  Dataset EGAD00001009744

• Single nucleus RNA sequencing of squamous cell carcinoma arising from mature teratoma of the ovary

  Squamous cell carcinoma arising from mature teratoma is one of the rare ovarian cancers. Therefore, the detailed molecular background of this disease has not been elucidated. The purpose of this study is to investigate the single-cell transcriptional landscape of this disease.

  Study JGAS000521