Command '['/work/b/cellranger-7.1.0/lib/bin/STAR', '--runMode', 'genomeGenerate', '--genomeDir', '/work/bio-wenzl/zebrafish111/star', '--runThreadN', '1', '--genomeFastaFiles', '/work/bio-wenzl/zebrafish111/fasta/genome.fa', '--sjdbGTFfile', '/work/bio-wenzl/zebrafish1...
Despite the emergence of experimental methods for simultaneous measurement of multiple omics modalities in single cells, most single-cell datasets include only one modality. A major obstacle in integrating omics data from multiple modalities is that diff
(with the pipeline used to process MET500 RNA-Seq data); in addition, we also re-processed the RNA-Seq data of another seven MDA-MB-231 cell line samples collected from SRA database. We re-performed TC analysis between the breast cancer cell lines (with re-processed data) and Basal-...
Human breast cancer data (TCGA) Derived from TCGA Research Network, URL: cancergenome.nih.gov/ Curated gene sets Obtained from Molecular Signatures Database, URL: gsea-msigdb.org/gsea/ms Additional information for reproducibility Available within the paper, extended data, source data, and supplementa...
Mouse Genome Database (MGD) 2019. Nucleic Acids Res. 2019;47:D801–6. Safran M, et al. GeneCards Version 3: the human gene integrator. Database (Oxford). 2010;baq020. Ding J, et al. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Nat Biotechnol. 2020;...
While cell QC removes background cells and problematic cells, the feature section is concerning genes. In the human genome, more than 20,000 genes are annotated, and mapped reads are counted for individual gene loci to yield the UMI count matrix. However, not all the > 20,000 genes ...
Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics Genome Biol 17.906 Langerhans cells are essential components of the angiogenic niche during murine skin repair Dev Cell 13.417 Retrotransposon instability dominates the acquired mutation landscape of mouse induce...
S7E). The subtype 4 epithelial markers specific for ASC were identical to the squamous cell carcinoma of other human cancers such as lung and cervical cancer from The Cancer Genome Atlas database (Fig. S7F, G). Taken together, these results demonstrate that KRTDAP and FAT2 serve as ...
When integrating bulk-RNA seq and scRNA-Seq screening signatures, the key difference from other methods like whole-genome sequencing (WGS) or whole-exome sequencing (WES) is that it focuses solely on gene expression rather than genomic variations or mutations. While WGS and WES provide valuable ...
Cell Genomics Scope The set of journals have been ranked according to their SJR and divided into four equal groups, four quartiles. Q1 (green) comprises the quarter of the journals with the highest values, Q2 (yellow) the second highest values, Q3 (orange) the third highest values and Q4 ...