23014 results for "ega"

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• Whole exome sequencing of sequential samples from a CLL patient over the course of venetoclax treatment, BCR inhibitor treatment, and venetoclax re-treatment

  The dataset contains whole exome sequencing data (libraries prepared using the Agilent SureSelect Human All Exon V6 kit, and paired-end sequenced on Illumina HiSeq4000 (2 x 150bp)) of 6 samples taken from peripheral blood mononuclear cells (PBMCs) (Samples 1-5) and bone marrow (BM). Data are provided as fastq files. Sample 1 was taken prior to initial venetoclax treatment. Sample 2 was taken as disease progression on venetoclax. Sample 3 was taken during response to BTK and PI3K inhibitor therapy. Sample 4 and the BM sample were taken at disease progression/prior to venetoclax re-treatment. And Sample 5 was taken during venetoclax re-treatment response.

  Dataset EGAD00001008685

• Immune profiling reveals enrichment of distinct immune signatures in oral epithelial dysplasia

  The dataset contains transcriptomic information of 36 oral potentially malignant disorders (OPMD), 14 fibroepithelial polyps (FEP), and 6 early stage oral squamous cell carcinoma (OSCC) from the Asian population. Total RNA was extracted from formalin-fixed paraffin embedded (FFPE) tissue sections. RNA libraries were prepared using the NEB NextUltra RNA kit with Illumina Ribo-Zero rRNA removal as per manufacturer’s instructions. RNA sequencing was performed on the HiSeq2500 platform to generate paired-end 150 nucleotides reads and with a coverage of 50 million reads per sample. Uploaded bam files have been mapped to the GRCh38 human genome using TopHat2. Clinical and demographic data for these patients are available from the associated publications or by request.

  Dataset EGAD00001007970

• Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells

  Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequenced normal cell DNAs from 10 individuals with MAP and study the somatic mutation burden and mutational signatures.

  Dataset EGAD00001007997

• Transcriptome and epigenome characterization of BMP signaling effects on H3.3K27M DIPG

  We profiled transcriptome and epigenome of BMP signaling effects on H3.3K27M DIPG.

  Dataset EGAD00001007768

• Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma

  In this study, we sequenced multiple stages of the B-lineage in elderly individuals and patients with lymphoplasmacytic lymphoma to study whether mutations are accumulated in normal-cell counterparts prior to lymphoma

  Dataset EGAD00001008196

• High hyperdiploid ALL single cell whole genome sequencing

  This dataset was collected from viable bone marrow cells obtained at diagnosis from nine patients with high hyperdiploid ALL and one normal bone marrow sample. All samples were subjected to low pass single cell whole genome sequencing with the median sequencing coverage of 0.02x. Single nuclei in G0/G1 phase were isolated using a fluorescence-activated cell sorting (FACS) cytometer. DNA libraries were constructed and associated next-generation sequencing was carried out by European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. Further details regarding the DNA libraries construction are available by Bos et. al., 2019 (https://link.springer.com/protocol/10.1007/978-1-4939-8931-7_15).

  Dataset EGAD00001008988

• Bone marrow microenvironment of 6 newly diagnosed myeloma patients using 10X Genomics scRNA- and TCR-sequencing

  10X Genomics scRNA- and TCR-sequencing (Chromium Next GEM Single Cell 5’ Reagent Kit v1.1) was performed on the plasma cell depleted mononuclear fraction of bone marrow aspirates from 6 patients with newly diagnosed multiple myeloma. Generated gene expression libraries were paired-end sequenced on the NovaSeq 6000 S2. Generated V(D)J libraries were paired-end sequenced on the NextSeq 550.

  Dataset EGAD00001009270

• Shallow whole genome sequencing and targeted capture sequencing data of PCNSL and PTL primary and relapse pairs

  Shallow whole genome sequencing for copy number analysis and targeted capture sequencing data for translocation and mutation anslysis of paired primary and relapse PCNSL and PTL samples

  Dataset EGAD00001008387

• Liver CD14+CD8+ T cells scRNAseq dataset

  Sorted single CD8+T cells expressing CD14 from human liver for SMARTSeq2. Livers processed: Kucykowicz et al STAR Prot 2022:pubmed.ncbi.nlm.nih.gov/35516846/ Published: Pallett et al Nature 2022 Tissue CD14+CD8+T-cells are reprogrammed by myeloid cells and modulated by LPS A modified SMART-seq2 protocol was performed on the single flow cytometry sorted-cells as previously described58. After cDNA generation, libraries were prepared (384 cells per library) using the Illumina Nextera XT kit (Illumina). Each library was sequenced to achieve a minimum depth of 1-2 million raw reads per cell using an Illumina HiSeq 4000 using v. 4 SBS chemistry to generate 75-bp paired-end reads.

  Dataset EGAD00001009831

• GEX CITE-Seq performance dataset

  To understand the impact of enzymatic treatments on gene expression and epitope preservation on major immune cell populations, skin dissociation (SkinD) and solid soft tumor dissociation (TumorD) were tested on three healthy PBMC samples in triplicate (D1, D2, D3), against an untreated control. CITE-seq performance was assessed on a solid biopsy cohort of 11 samples (5 healthy skin samples, 3 primary melanoma samples, 3 melanoma metastasis samples) as well as on a liquid biopsy PBMC cohort consisting of three healthy donors and three immunotherapy-treated melanoma patients. This dataset contains the GEX data for each sample. Data is provided in the form of pooled BAM files. Linkage between samples, BAM files and hashtags is provided in a separate linkage file.

  Dataset EGAD00001008418