Gene expression and splicing counts from the Yepez, Gusic et al study - fibroblast, hg19, strand-specific, low seq depth

<p><strong>File description:</strong></p> <ol> <li> <p>geneCounts: gene-level counts&nbsp;</p> </li> <li> <p>k_j: split counts spanning from one exon to another.</p> </li> <li> <p>k_theta: non-split counts covering a splice site</p> </li> <li> <p>n_psi3: total split counts from a given acceptor site</p> </li> <li> <p>n_psi5: total split counts from a given donor site</p> </li> <li> <p>n_theta: total split and non-split counts for a given splice site</p> </li> <li> <p>Sample annotation describing each sample from the dataset</p> </li> <li> <p>Description file with global information from the dataset</p> </li> </ol> <p>The gene counts were originated using the GTF file from release 34 of GENCODE&nbsp;<a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a>, and the split and non-split counts contain only the annotated junctions from the same release.</p> <p><strong>Use:&nbsp;</strong>The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, DROP&nbsp;can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>).</p> <p><strong>Number of samples:</strong> 127<br> <strong>Tissue:</strong> Fibroblast<br> <strong>Organism:</strong> Homo sapiens<br> <strong>Genome assembly:</strong> hg19<br> <strong>Gene annotation:</strong> gencode34</p> <p><strong>Median mapped reads:</strong>&nbsp;71 million<br> <strong>Disease</strong> (ICD-10: N): E88: 84, NONE: 12, F89: 6, G31: 3, R27: 3, E72: 3, G40: 2, R16: 2, K72: 2, P94: 2, E77: 1, E75: 1, G71: 1,&nbsp;G93: 1, Q78: 1, G82: 1, R29: 1, Q02: 1<br> <strong>Strand specific:</strong> True<br> <strong>Paired end:</strong> True</p> <p><strong>Dataset contact:</strong>&nbsp;Vicente Yepez, yepez at in.tum.de; Christian Mertes, mertes at in.tum.de; Julien Gagneur, gagneur at in.tum.de; Holger Prokisch, prokisch at helmholtz-muenchen.de</p> <p><strong>Citation:</strong>&nbsp;Cite both the resource using Zenodo&#39;s citation&nbsp;and the publication under References</p> <p>&nbsp;</p>