11925 results for "cancer rna-seq"

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• NIMH Human Middle Temporal Gyrus (MTG) Cell Types

  Elucidating the cellular architecture of the human neocortex is central to understanding our cognitive abilities and susceptibility to disease. In this study, we applied single nucleus RNA sequencing to perform a comprehensive analysis of cell types in the middle temporal gyrus of human cerebral cortex. We identify a highly diverse set of excitatory and inhibitory neuronal types, many of which are relatively sparse. Additionally, we found that excitatory types are less layer-restricted than expected based prior knowledge from cell morphologies and from mouse studies. Comparison to a similar mouse cortex single cell RNA-sequencing dataset revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of human cell type properties. Despite this general conservation, we also find extensive differences between homologous cell types in human and mouse, including dramatic alterations in proportions, laminar distributions, gene expression, and morphology. These species-specific features emphasize the importance of directly studying human brain. This study conducted by the Allen Institute for Brain Science was supported by the Allen Institute for Brain Science and by US National Institutes of Health grant U01 MH114812-02 to E.S.L. Collaborators request that publications resulting from these data cite their original publication: Hodge RD, Bakken TE, et al. Conserved cell types with divergent features between human and mouse cortex. bioRxiv. 2018 doi: 10.1101/384826.

  Study phs001790

• PML complete dataset

  We generated single-cell transcriptomics, single-nuclei chromatin accessibility, CITE-seq and Multiomics of patients with PML. Pools are genetically multiplexed across donors, genotypic variation is included in this dataset to enable demultiplexing.

  Dataset EGAD50000000197

• Cord blood progenitor CITE-seq dataset

  Sequencing results of single-cell transcriptome and antibody libraries from two biological experiments of cord blood progenitor cells. Four samples from different time points were processed using 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Gene expression and antibody-derived libraries were sequenced separately.

  Dataset EGAD50000000405

• EBNA2 ChIP-Re-ChIP in primary B-cells infected with EBV virus

  EBNA2 ChIP-Re-ChIP in primary bulk B cells 4 days post EBV-infection with B95-8. DNA binding elements of the viral master regulator EBNA2, EBNA2-CBF transcription factor complex or EBNA2-EBF1 transcription factor complex were analyzed to identify virally targeted genes.

  Dataset EGAD50000000301

• Target sequencing of 53 synovial sarcoma patients

  This dataset contains 138 .bam files sequenced with Illumina NovaSeq 6000. The files with the variant calling performed to the sequencing data, as well as the clinical data (phenotype) extracted during the sample extraction.

  Dataset EGAD50000000743

• Strand-seq data of six CK-AML patient samples and three matching PDXs

  We performed strand-specific single-cell sequencing of six primary leukemia samples from four CK-AML patients. We also performed strand-specific single-cell sequencing of three matching patient-derived xenografts (PDXs). The dataset contains BAM files for each cell.

  Dataset EGAD50000000634

• scRaCH-seq fastq files

  We base called the raw data of nanopore sequencing using the Guppy software (v3.1.5) with “dna_r9.4.1_450bps_sup_prom.cfg” configuration. The passed reads (Qscore > 9) are deposited in this EGA study.

  Study EGAS50000000165

• Dataset of Recurrent resistance mutations to lirafugratinib delineate treatment sequences for FGFR2-driven tumors

  This dataset is made of 23 pairs of RNAseq and 36 pairs of Exome-seq, both sequenced from Illumina Novaseq. This includes 47 samples, composed of 25 tumors, 13 healthy and 9 xenograft

  Dataset EGAD50000001981

• BLUEPRINT Methylome saturation and COMET analysis of monocyte samples

  Bisulfite-Seq of CD14-positive, CD16-negative classical monocyte samples for methylome saturation and COMET analysis

  Dataset EGAD00001001261

• Tam-seq of germline samples for HGSOC copy-number signatures study

  This dataset contains targeted amplicon sequencing of Germline DNA extracted from 56 blood samples. They were sequenced on Illumina HiSeq 2500 and aligned to human genome assembly GRCh37 (hg19)to produce 127 bam files (2-3 technical replicates per sample).

  Dataset EGAD00001004172