Pediatric Tumor Affymetrix Gene Expression

{"name":"Zeisel/layout_data_10gene_uq_7550","dataSubType":"Map","cohort":"Single-cell RNA-seq mouse cortex (Zeisel)","label":"TSNE map","description":"The map is built by bhtsne method using 9694 genes that are expressed in >10% cells in this study. The sample x gene data matrix is from the normalized dataset in this cohort. Barnes-Hut implementation of the t-SNE algorithm: https://github.com/lvdmaaten/bhtsne/.","type":"clinicalMatrix","version":"2017-03-15"}

{"name":"Zeisel/Zeisel_expression_log2.uq_7750","dataSubType":"gene expression RNA-seq (single-cell)","cohort":"Single-cell RNA-seq mouse cortex (Zeisel)","label":"mouse cortex and hippocampus single-cell RNA-seq (normalized)","description":"Zeisel expression data is log2(x+1) transformed. For each cell, gene expression is upper quartile normalized (75 percentile) using 824 genes that are expressed in >70% cells in this study, then scaled with value of 75 percentile -50 percentile of the 824 genes' expression value","type":"genomicMatrix","version":"2017-03-15","unit":"log2(count-uq+1)","pseudocount":1}

{"cohort":"Single-cell RNA-seq mouse cortex (Zeisel)","url":"http://science.sciencemag.org/content/347/6226/1138, http://linnarssonlab.org/cortex/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60361, https://storage.googleapis.com/linnarsson-lab-www-blobs/blobs/cortex/expression_mRNA_17-Aug-2014.txt","dataSubType":"gene expression RNA-seq (single-cell)","citation":"Science  06 Mar 2015: Vol. 347, Issue 6226, pp. 1138-1142 DOI: 10.1126/science.aaa1934","pubmed":"25700174","label":"mouse cortex and hippocampus single-cell RNA-seq","articletitle":"Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq","name":"Zeisel/Zeisel_expression_mRNA_log2","type":"genomicMatrix","version":"2017-03-03","unit":"log2(count+1)","description":"<b>Publication Abstract</b><br><br>The mammalian cerebral cortex supports cognitive functions such as sensorimotor integration, memory, and social behaviors. Normal brain function relies on a diverse set of differentiated cell types, including neurons, glia, and vasculature. Here, we have used large-scale single-cell RNA sequencing (RNA-seq) to classify cells in the mouse somatosensory cortex and hippocampal CA1 region. We found 47 molecularly distinct subclasses, comprising all known major cell types in the cortex. We identified numerous marker genes, which allowed alignment with known cell types, morphology, and location. We found a layer I interneuron expressing Pax6 and a distinct postmitotic oligodendrocyte subclass marked by Itpr2. Across the diversity of cortical cell types, transcription factors formed a complex, layered regulatory code, suggesting a mechanism for the maintenance of adult cell type identity."}