10x genomics visium pipeline instructions  (10X Genomics)

Journal: Communications Biology

Article Title: Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets

doi: 10.1038/s42003-024-05877-4

Figure Lengend Snippet: a – h USC control sample sequenced by three library preparation methods: bulk RNA-Seq with ribosomal depletion, bulk RNA-Seq without ribosomal depletion (polyA), and spatial transcriptomics (10x Visium platform). i – l All GEO+ samples ( n = 463); ( m–p ) all GTEx samples ( n = 1107). Definitions: Total RNA-Seq Reads = FASTQ reads prior to alignment; MT Benchmark Coverage = average mitochondrial sequencing depth measured from two 250 bp segments within the RNR1 and CYB genes ; Deletion Read Rate = deletion reads/MT Benchmark Coverage. MTG (middle temporal gyrus); AM (amygdala); SN (substantia nigra); TL (temporal lobe); DLPFC (dorsolateral prefrontal cortex); CER (cerebellum); HIPP (hippocampus); PFC (prefrontal cortex); VTA (ventral tegmental area); LCM (laser capture microdissection); PD (Parkinson’s Disease); CTRL (control); AD (Alzheimer’s Disease); SCZ (schizophrenia); BD (bipolar disorder); MDD (major depressive disorder). Abbreviations for GTEx tissues are shown on figure.

Article Snippet: Spatial transcriptomics datasets were processed using the 10x Genomics Visium pipeline instructions ( https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome ).

Techniques: Control, RNA Sequencing, Sequencing, Laser Capture Microdissection

Journal: Communications Biology

Article Title: Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets

doi: 10.1038/s42003-024-05877-4

Figure Lengend Snippet: Summary of 12 GEO + RNA-Seq datasets evaluated for mtDNA deletions

Article Snippet: Spatial transcriptomics datasets were processed using the 10x Genomics Visium pipeline instructions ( https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome ).

Techniques: Control, Sample Prep, Hybridization, FACS