12405 results for ""non-traditional+communal+storytelling+approach"+novel+segment+noted+in+critical+commentary"

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• Single-Cell Sequencing of Genomic DNA, RNA, and ADT in CRISPR-Edited Cells

  CRAFTseq data containing multi-modal single-cell genomic DNA amplicon, cDNA and surface-protein from various primary cell types and cell lines, including human CD4 T cells, Jurkat cells, HH cells, Daudi cells and HEK293T cells. Cells were edited with CRISPR HDR or base editing. Also contains bulk RNA-seq data for edited human primary CD4 T cells and Daudi cells.

  Study phs004042

• M116 Microbiome data

  M116 stool was collected from 3 different days (3 biological replicates) and kept at -20ºC until DNA extraction (Biobanc IDIBGI and Goodgut®). Total genomic DNA was extracted from 150–200 mg of each stool sample after homogenisation using the DNeasy Powersoil Pro kit (Qiagen®) according to manufacturer’s instructions. Quality and quantity of DNA were evaluated using Qubit® BR kit on a Qubit®2.0 fluorimeter (ThermoFisher Scientific®) and on a Nanodrop ND-2000 UV-Vis spectrophotometer (ThermoFisher Scientific®). The v3-v4 region of the bacterial 16S rRNA gene was amplified and sequenced (paired-end 250-bp) following standard practices at external facilities (Novogene®) using previously described primers 515F. Files types included in this dataset are raw Fastq files.

  Dataset EGAD50000001288

• Ribosomal profiling on Epstein-Barr virus transformed B-lymphoblastoid cell lines.

  This dataset contains Ribo-seq BAM files of Epstein-Barr virus-transformed B-lymphoblastoid cell lines from six individuals (HG00114, HG00282, NA12005, NA12044, NA12717 and NA12751) of the GEUVADIS Project. For each EBV-LCL, 20 million cells were treated with 2 μg/ml harringtonine and 100 μg/ml cycloheximide. After lysing cells in lysis buffer supplemented with 100 μg/ml cycloheximide, ribosome complexes were purified by density purification. Small RNA molecules were isolated using the NucleoSpin miRNA Kit (Bioke, Leiden, Netherlands), followed by RNA PAGE gel separation. Universal linkers were added after dephosphorylation. After reverse transcription, the cDNA was circularized and, after ribosomal RNA depletion, barcoded and sequenced on Illumina NextSeq 500.

  Dataset EGAD50000000465

• Transcriptomic profiling of T cells following ABHD11 inhibition

  This dataset contains paired-end RNA sequencing data from human T cells treated with ML226, a selective ABHD11 inhibitor, and matched vehicle controls. The experiment was designed to investigate the role of ABHD11 in sterol metabolism and its impact on T cell effector function and autoimmunity. Samples were collected across biological replicates following 24-hour treatment, and RNA was extracted for high-throughput sequencing. Sequencing was performed using an Illumina platform. The dataset supports analysis of differentially expressed genes, alternative transcript usage, and pathway-level effects of ABHD11 inhibition. This dataset is part of the study titled "ABHD11 inhibition drives sterol metabolism to modulate T cell effector function and alleviate autoimmunity".

  Dataset EGAD50000001845

• GeoMx DSP of NGS mRNA expression in pre-treatment biopsies from patients with metastatic triple-negative breast cancer treated with PARP inhibitors.

  This dataset contains GeoMx digital spatial profiling (DSP) data from 12 FFPE pre-treatment biopsies of metastatic HR-altered breast cancer patients subsequently treated with PARP inhibitors (Olaparib or Talazoparib). Samples were collected from primary breast tumors (n=7) and metastatic sites including lymph nodes (n=2), bone (n=2), and brain (n=1). Tissue sections were stained for pan-cytokeratin (PANCK) to selectively profile tumor cells, with NGS-based transcriptome data generated for both PANCK+ and PANCK- regions. The dataset includes raw data files (176 fastq files) along with clinical annotations.

  Dataset EGAD50000001932

• RoCK and ROI single-cell transcriptome of one acute lymphoblastic leukemia patient

  Whole-transcriptome single-cell RNA sequencing (scRNA-seq) was performed following the manufacturer’s protocol (BD Rhapsody, BD Biosciences). Targeted enrichment of BCR::ABL1 transcripts was conducted using the RoCK and ROI-seq approach, based on the barcoded bead technology of the BD Rhapsody platform. In the RoCK and ROI-seq workflow, the template-switch oligonucleotides (TSOs) attached to BD Rhapsody beads were modified with one or multiple capture sequences specific to transcripts of interest, enabling targeted transcript capture during reverse transcription. ROI primers that are added during library preparation to direct amplification and sequencing toward these defined regions of interest (ROIs). Resulting libraries were sequenced on an Illumina sequencer.

  Dataset EGAD50000001976

• RNA-seq of oropharynx cancer cases from University of Michigan

  This dataset consists of 67 bulk RNA-seq data (sorted aligned BAM files) from formalin-fixed paraffin-embedded (FFPE) oropharynx tumor samples from the University of Michigan (UM). Samples were collected as part of the UM Head and Neck SPORE between 2008-2014. Library preparation was performed using the ribo-depletion method with the FastSelect kit and sequenced on the NovaSeq 6000 at the UM Advanced Genomics Core, resulting in 150bp paired-end reads. Raw reads were trimmed using Cutadapt (v3.4) and aligned to hg38 and high-risk HPV genomes using STAR (v2.7.9a). 62 of 67 samples were determined to be HPV RNA-positive.

  Dataset EGAD50000001306

• Summarized somatic variant calls from CMMRD-associated high-grade gliomas

  This dataset contains summarized somatic variant call data derived from paired tumor–blood whole-exome sequencing of human samples. Access to the dataset is controlled and granted only upon submission and approval of a formal data access request. Requests are reviewed by the Data Access Committee led by the Principal Investigator to ensure compliance with applicable legal, ethical, and data protection requirements. Users must not attempt to re-identify study participants and must comply with all relevant confidentiality and data protection regulations. In accordance with local legal and ethical requirements, individual-level raw sequencing data are not shared.

  Dataset EGAD50000002180

• Bulk RNAseq FASTQ files of three PDAC organoid lines treated with LGK974 or DMSO for 24h

  This dataset contains raw FASTQ files from bulk RNA sequencing of three patient-derived pancreatic ductal adenocarcinoma (PDAC) organoid lines (P28, P40, P47). Each organoid line was treated with either the WNT secretion inhibitor LGK974 or DMSO for 24 hours, with three biological replicates per treatment condition. RNA was extracted using the Qiagen QiaSymphony SP system, and libraries were prepared with the Illumina Truseq stranded polyA kit. Sequencing was performed on an Illumina NextSeq2000 platform using single-end 50bp reads. Quality control was conducted with FastQC, and reads were trimmed with TrimGalore as appropriate. Data are controlled-access and intended for transcriptomic analysis of WNT pathway perturbation in PDAC organoid models.

  Dataset EGAD50000002219

• scMethylation data of 5 regionally sampled GBM tissue for 2 patients

  This dataset contains snRNA-seq data of 5 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed in an unbiased manner without any sorting procedure. Nuclei dissociation was performed following the nuclei isolation for single-cell ATAC-seq (10x Genomics; CG000169) with matched peri-tumoral and tumor core samples. Subsequent single-cell methylation sample preparation followed Scale Biosciences single-cell methylation kit protocol v1.0. mplification adaptors through ligation and adding a second barcode though indexed PCR reaction following Scale Biosciences single-cell methylation kit protocol v1.0. We employed the TWIST human methylome panel for targeted enrichment of informative methylation sites.

  Dataset EGAD50000001837

• Single-cell transcriptome analysis of B-cell development in the ABO platform

  The dataset includes samples from four individual donors, pooled at each cell-harvesting time point (days 21, 28, and 35). Single-cell RNA sequencing was performed on the 10x Genomics Chromium platform using GEM-X Single Cell 5′ v3 and GEM-X Single Cell V(D)J v3 for BCR profiling. For each timepoint, paired libraries were constructed: a 5′ GEX library and a V(D)J-B library. Per reaction 350,000-400,000 cells were loaded, aiming for 60,000 cells per reaction. Pooled libraries were sequenced on an Illumina NovaSeq X sequencer. 50,000 read pairs per cell for GEX and 5,000 read pairs per cell for V(D)J were targeted.

  Dataset EGAD50000002433

• Genomic and transcriptomic profiling of signalling networks in follicular lymphoma

  This dataset is composed of sequencing data from 16 patients diagnosed with follicular lymphoma, who developed transformed disease and for whom representative frozen tumor biopsy samples were available. For 14 patients there is paired material from both disease stages. DNA and RNA libraries were constructed and captured with a kinome bait library (Agilent Technologies), before sequencing on an Illumina platform.

  Study EGAS00001002175

• Whole-genome bisulfite sequencing analysis of low-grade astrocytomas in the ICGC PedBrain Tumor Project

  Pilocytic Astrocytoma (PA) is the most common pediatric brain tumor. While genome and transcriptome landscapes are well-studied, data of the complete methylome, tumor cell composition and immune infiltration are scarce. We generated whole genome bisulfite sequence data (WGBS) of nine PAs to find evidence for a link of focal methylation differences and differential gene expression to immune infiltration.

  Study EGAS00001004019

• Transcriptomic and epigentic analysis of human peripheral blood NK cell subsets revealing role of Bcl11b in differentiation

  Transcriptomic analysis of seven human peripheral blood NK cell subsets and three T cell subsets purified from healthy cytomeglovirus seropositive donors. Epigenetic analysis including identification of open chromatin and active enhancer elements confirms key regulatory factors defining an NK cell differentiation axis. Chromatin-immunoprecipitation sequencing reveals contribution of key transcription factors associated with NK cell differentiation including Bcl11b.

  Study EGAS00001005025

• RNA-seq following miR-130a overexpression (OE) in human CD34+cord blood cells

  We performed RNA-seq on CD34+ human cord blood (CB) cells transduced with Control or miR-130a OE lentiviruses to identify differentially expressed genes. Sorted CD34+ cells from 3 independent cord blood pools were transduced with lentiviruses containing mOrange (mO) reporter gene. mO+ cells were sorted 3 days post-transduction and RNA was harvested for library preparation and sequencing.

  Study EGAS00001005868

• Extensive patient-to-patient single nuclei transcriptome heterogeneity in pheochromocytomas and paragangliomas

  Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors of varied genetic makeup, associated with high cardiovascular morbidity and a variable risk of malignancy. We focused on PCPG tumors with germline SDHB and RET mutations, representing distinct prognostic groups with worse or better prognoses, respectively. We applied single-nuclei RNA sequencing (snRNA-seq) on tissue samples from 11 patients.

  Study EGAS00001006230

• A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours

  We generated a single-cell RNA-seq atlas capturing over 100,000 cells spanning all stages of the mouse cerebral development. By examining data from over 100 cerebral tumour samples, our study reveals that, despite the phenotypic/genotypic differences between the tumour types, they are all comprised of developmental sublineages that map most closely to embryonic or juvenile stages of development.

  Study EGAS00001006237

• Understand Paratyphoid Disease - host responses to human challenge with S. Paratyphi A (2019-08-28)

  This project aims to evaluate the transcriptional response to disease measured in whole blood of participants who developed enteric fever after challenge and, importantly, those who were challenged but stayed well throughout the challenge period. This data will provide unique coverage of the transcriptome and will yield invaluable insight after integration with a wealth of clinical data collected during this trial. 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 2019-08-28.

  Dataset EGAD00001005298

• RNA-seq of iPSC-derived oligodendrocytes of individuals with and without t(1;11) translocation

  This dataset contains high-throughput RNA-sequencing of 14 samples, each sample comprising oligodendrocytes derived from human induced pluripotent stem cells, from individuals with and without a balanced t(1;11) translocation which substantially increases risk of major mental illness. 5 samples derive from 2 control individuals, and 9 samples from 3 individuals carrying the translocation. Libraries were prepared from each total-RNA sample using the TruSeq Stranded Total RNA with Ribo-Zero kit. Libraries were then sequenced using the NextSeq 500/550 High-Output v2 (150 cycle) Kit on the NextSeq 550 platform. Raw paired-end sequencing data is stored in two FASTQ files per sample.

  Dataset EGAD00001006341

• Plasma whole genome sequencing from patients with stage IV colorectal cancer and microsatellite instability

  This dataset contains plasma WGS data from patients with stage IV colorectal cancer (CRC, n = 16) and healthy individuals (n = 21) used in the Pointy manuscript. Patients with CRC provided written consent and samples were collected as performed as described previously (Clinical-Trials.gov number NCT01876511; Georgiadis et al., 2019, Le et al., 2017). Plasma samples from 21 healthy control individuals were procured through BioIVT. Cell-free DNA (cfDNA) was extracted from plasma using the QIAamp Circulating Nucleic Acid Kit. Libraries were prepared with 5 to 250 ng of cfDNA using the NEBNext DNA Library Prep Kit. Libraries were sequenced on HiSeq2000/2500.

  Dataset EGAD00001008999

• WES and RNAseq of Simultaneous Bilateral Breast Cancer

  This dataset includes NGS profiling of 13 women with simultaneous bilateral breast cancer. Seven women have WES of untreated surgical resections and matched healthy tissue. The six other women have WES of healthy tissue, WES+RNAseq of pre-neoadjuvant tumor biopsies, and when residual disease was present (6 tumors in 4 patients), WES+RNAseq of residual disease from post-neoadjuvant therapy surgery. One patient from the WES+RNAseq cohort had multifocal bilateral disease at diagnosis so there are 2 pre-neoadjuvant biopsy samples from each breast.

  Dataset EGAD00001009987

• RNAseq of blood, fat and muscle samples from 45,X, 46,XX, 46,XY and 47,XXY

  Samples of blood, muscle and fat were collected from individuals with TS (n = 33) and KS (n = 22) and from male (n = 16) and female (n = 44) controls. The RNA-seq libraries were multiplexed paired-end sequenced on an Illumina Novaseq 6000 (100 bp) and subjected to initial quality control using FastQC (BAbraham Bioinformatics). In addition to trimming of low-quality ends, adaptor removal was conducted using Trim Galore with default settings (BAbraham Bioinformatics).

  Dataset EGAD00001010052

• EPICC: Evolutionary Predictions in Colorectal Cancer

  661 bam files generated from high-throughput RNAseq of tumour biopsies from colorectal cancer patients

  Dataset EGAD00001007828

• Dataset for upper_gastrointestinal_tumor-RNA

  Rare cancer sequencing data of 44 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008853

• CD19 CAR-T cells from non-Hodgkin's lymphoma patients

  The samples across 17 NHL patient samples with the CD19 CAR-T treatments are sequenced in 10x genomics. Refer to the manuscript supplementary tables and "https://github.com/hwanglab/hwanglab_2021_tigitCarT" for the sequencing sample sheets, the patient clinical information, processed data, and source codes.

  Dataset EGAD00001007741