23225 results for "ega"

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• Transcriptional profiles of Kleefstra syndrome (EHMT1 and EHMT2) and healthy fibroblasts

  This dataset contains FASTQ files from RNA sequencing (RNA-seq) of fibroblasts derived from a healthy donor (control), a patient with Kleefstra syndrome (KSP), and a patient carrying a pathogenic variant in EHMT2 (P2). Ribosomal RNA was removed using an RNase H–based depletion method, and strand-specific libraries were prepared for paired-end sequencing on the MGI DNBSEQ PE100 platform.

  Dataset EGAD50000002343

• Transcriptional profiles of Kleefstra syndrome (EHMT1 and EHMT2) and healthy iPSCs

  This dataset contains FASTQ files from RNA sequencing (RNA-seq) of induced pluripotent stem cells (iPSCs) derived from a healthy donor (control), a patient with Kleefstra syndrome (KSP), and two patients carrying pathogenic variants in EHMT2 (P1 and P2). Poly(A)-selected RNA was used for library preparation, and strand-specific libraries were generated for paired-end sequencing on the MGI DNBSEQ PE100 platform.

  Dataset EGAD50000002344

• WNT7B-reporter organoids sorted

  Transcriptomic data from pancreatic ductal adenocarcinoma (PDAC) organoids to investigate the role of WNT7B. This dataset includes: - Bulk mRNA sequencing of WNT7B-reporter pancreatic ductal adenocarcinoma (PDAC) organoids sorted for cells displaying low, medium and high expression of the reporter

  Study EGAS50000001543

• Bulk RNA sequencing data of high-grade serous ovarian cancer samples (set 18-19)

  The dataset contains RNA sequencing data of 66 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 155 samples are fresh frozen tissue samples that have been collected from different tissues and time points before and during treatment. The files provided are paired fastq files.

  Dataset EGAD50000002370

• Case Report: Pre-Clinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma

  We report a rare case of a young patient (VENUS 167) initially diagnosed with grade 1 endometrioid endometrial cancer, which, following endocrine treatment, presented with mixed aggressive carcinoma with three distinct histologic patterns: grade 1 endometrioid, large cell neuroendocrine, and undifferentiated carcinoma. The NGS fastq data are WES, RNAseq and ATAC

  Dataset EGAD50000002397

• Transcriptome analysis of human muscle/myofibers carrying the human nemaline myopathy type 6-associated KBTBD13-R408C variant.

  This dataset contains mRNA-seq results from eleven samples from human donors, each sample being composed of 5-10 rebulked fiber type-specific myofibers. This sample set includes; 1) Three FT-I and three FT-IIa rebulked samples from control individuals 2) Three FT-I and two FT-IIa rebulked samples from NEM6 patients with a KBTBD13R408C variant (NP_001094832.1: p.Arg408Cys)

  Dataset EGAD50000002408

• BAM-format HiFi whole genome sequencing reads (PacBio Revio) from stabilized human saliva

  HiFi whole‑genome sequencing data from a single human saliva sample collected and stabilized using an Oragene device. Sequencing was performed on a SMRT® Cell using PacBio Revio™ SPRQ chemistry. Sequencing produced >100 Gb of HiFi reads yielding >30× genome coverage suitable for comprehensive variant and methylation analysis. Dataset includes long‑read HiFi sequences in BAM format, containing both aligned and unaligned reads.

  Dataset EGAD50000002398

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set5)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of four hyperdiploid ALL patients (ALLT-502, ALLK-130, ALLK-137, ALLK-139). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq X Plus.

  Dataset EGAD50000002428

• Whole Genome Methylation in CLL

  We have extensively characterized the DNA methylome of chronic lymphocytic leukemia (CLL) with mutated and unmutated IGHV as well as several mature B cell subpopulations using whole-genome bisulfite sequencing and high-density microarrays.

  Study EGAS00001000272

• Whole exome sequencing of virus-associated HCC

  To understand comprehensive combinations of molecular alterations and seek for potential therapeutic targets/pathways in virus-associated HCC, we have conducted a whole exome sequencing (in-solution capturing all human coding exons) of 150 pairs of HCC cases.

  Study EGAS00001000389

• Multiomic cell-free DNA profiling to inform molecular classification and immunotherapy outcomes in endometrial cancer

  This study involved a cell-free DNA (cfDNA) framework integrating genomic, transcriptomic and epigenomic profiling to investigate patient response to immune checkpoint inhibitors in advanced endometrial cancer (EC) with mismatch repair deficiency (dMMR).

  Study EGAS50000001582

• Spatially resolved transcriptomics reveals profound subclonal heterogeneity and T cell dysfunction in extramedullary myeloma

  Investigating the spatial architecture and microenvironment of EMD lesions in Multiple Myeloma patients using spatial whole transcriptome sequencing (10X Visium), tomography for spatially resolved transcriptomics (TOMO-seq), and single-cell RNA sequencing (scRNAseq)

  Study EGAS50000000227

• TenK10K Phase 1: Whole Genome Sequencing Alignments

  Whole genome sequencing was performed for 1,925 samples from phase 1 of the TenK10K project. Sequencing was done with Illumina 2 x 150bp chemistry on a NovaSeq 6000 instrument to achieve mean 30x coverage. Sequence reads were aligned to the GRCh38 reference assembly with a fork of DRAGMAP v1.3.1. This dataset is comprised of 1,925 alignment files in cram format, and their corresponding index files.

  Dataset EGAD50000002466

• Arkansas Children’s Research Institute (ACRI) Data Access Committee – Kelly Research Group

  The Arkansas Children’s Research Institute (ACRI) Data Access Committee – Kelly Research Group oversees requests for access to controlled human genomic and transcriptomic data generated by the Kelly Research Group. The committee ensures that all data access requests are consistent with participants’ informed consent, institutional review board (IRB) approvals, and applicable regulatory requirements. All approved users must agree to use the data solely for biomedical research purposes, maintain data confidentiality, and acknowledge the data source in resulting publications.

  Dac EGAC50000000819

• Whole genome bisulfite sequencing of hepatitis B virus-associated hepatocellular carcinoma tumor and non-cancerous samples

  To understand comprehensive epigenetic alterations in hepatitis B virus-associated HCC, we have conducted a whole genome bisulfite sequencing of 5 tumor samples and 3 non-cancerous samples (3 pairs and 2 tumors).

  Study EGAS00001002230

• Single-cell profiling maps the spectrum of crosstalk between glioma cells and tumor associated macrophages

  Tumor associated macrophages (TAMs) are a heterogeneous glioma infiltrate, implicated in cancer progression. We performed single-cell RNA-sequencing, to survey TAM response-patterns in glioma.

  Study EGAS00001002185

• Genetic landscape of pediatric ependymoma

  We performed whole-genome sequencing of 42 paired tumor/normal EPD genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000254

• RNA-Sequencing data of patient derived normal fibroblasts (NFs), cancer associated fibroblasts (CAFs) and tumor spheroid samples

  RNA-Sequencing data of patient derived normal fibroblasts (NFs), cancer associated fibroblasts (CAFs) and tumor spheroid samples performed in the context of the characterization of an IL1R1 positive CAF population in CRC tumour samples.

  Study EGAS00001007205

• Mutational_burden_in_skin_following_UV_treatment_Nanoseq

  We wish to assess the changes in mutational burden in patients under going UV treatment for psoriasis. Using duplex sequencing we will assess mutational burden in traditionally sun exposed (arm) and non-sun exposed (buttock) skin epidermis both pre and post UV treatment.

  Study EGAS00001007681

• 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

• HER2_positive_Breast_Cancer_

  We propose to definitively characterise the somatic genetics of HER2+ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000042

• BGISEQ-500 Cancer Dataset - WGS tumour/normal pairs

  This study contains whole genome sequencing data for 3 matched tumour / normal pairs from Mesothelioma patients. The sequencing is 50bp paired-end generated using the BGISEQ-500 and is provided as 6 aligned and duplicate-marked BAM files.

  Study EGAS00001002298

• Matched_Pair_Cell_Line_Tumour_RNAseq

  In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Study EGAS00001000434

• Genetic_factors_underlying_premature_MI_in_Greek_families_without_vessel_disease

  The study will analyse by exome sequencing 8 Greek family members with an excess of potentially damaging mutations relating to premature MI and no vessel disease, to identify genetic factors underlying this condition. This is a follow on from project GPMI-NVD

  Study EGAS00001000478

• Spectrum and significance of MYC and BCL2 mutations in DLBCL

  We analyzed the spectrum and clinical significance of MYC and BCL2 mutations in 347 DLBCL cases from population-based cohort of BC, Canada. Mutational status of MYC and BCL2 coding exons were sequenced using TSCA assay.

  Study EGAS00001002206