Adult Mouse Olfactory Bulb
Spatial Gene Expression dataset analyzed using Space Ranger 1.3.0
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10X Genomics obtained fresh frozen mouse olfactory bulb tissue from BioIVT. 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, then fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).
- Sex: Male
- Age: >8 weeks
- Strain: C57BL/6
- Section Orientation: Coronal
The H&E image was acquired using a Hamamatsu NanoZoomer S60 digital slide scanner with the following settings:
- Brightfield camera
- 20X objective
The Visium Gene Expression library was prepared as described in the Visium Spatial Reagent Kits User Guide (CG000239 Rev D). Sequencing data was processed using Space Ranger.
- Sequencing instrument: Illumina NovaSeq 6000, flow cell HCCN5DSX2 (lanes 1-4)
- Sequencing depth: 39,560 mean reads per cell
- Sequencing configuration: Paired-end (28 X 90), Dual-Indexed Sequencing. Read 1: 28 cycles (16 bp barcode, 12 bp UMI); i7 index: 10 cycles; i5 index: 10 cycles; Read 2: 90 cycles (transcript).
- Dual-Index set: T1T2-A9
- Slide: V10N30-322
- Area: A1
Key metrics were:
- Spots detected under tissue: 1,185
- Median genes per spot: 4,790
- Median UMI counts per spot: 16,029
This dataset is licensed under the Creative Commons Attribution license.