Human Cerebellum: Targeted-Compare, Neuroscience Panel

10X Genomics obtained fresh frozen human cerebellum tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

Visium whole transcriptome gene expression libraries (T1T2-E2) were prepared as described in the Visium Spatial Reagent Kits User Guide (CG000239 Rev D) and sequenced on a NovaSeq 6000.

Targeted libraries were prepared following the Targeted Gene Expression - Spatial User Guide (CG000377) using the Human Neuroscience Panel (PN-1000278) and sequenced on a NovaSeq 6000.

The targeted-compare pipeline in Space Ranger was used to compare the parent whole transcriptome analysis (WTA) with the neuroscience targeted analysis. While it is not necessary to compare the WTA and targeted data when doing targeted gene expression, if both the targeted and parent samples have been sequenced, the targeted-compare pipeline may be used to compare the two samples.

Key metrics were:

• Mean Reads per Tissue-Covered Spot: 10,200 (targeted); 42,431 (WTA)
• Median Targeted Genes per Tissue-Covered Spot: 288 (targeted); 269 (WTA)
• Median Targeted UMIs per Tissue-Covered Spot: 625 (targeted); 580 (WTA)
• Mean UMI recovery ratio (targeted vs. parent): 1.139
• Pearson correlation of log10 UMI counts per gene: 0.993

To maintain donor anonymity, sequence data for this sample is not currently available.

This dataset is licensed under the Creative Commons Attribution license.