High-throughput mapping of long-range neuronal projection using in situ sequencing, Chen et al., dataset 2

Published: 4 October 2019| Version 1 | DOI: 10.17632/g7kdxznt6w.1
Xiaoyin Chen


Raw in situ sequencing data and other images for the paper of the same name. Part of four related datasets: 10.17632/mk82s9x82t.1 10.17632/g7kdxznt6w.1 10.17632/86wf7xfz5x.1 10.17632/2w649fccnt.1 These datasets demonstrate BARseq, a highly multiplexed projection mapping method based on in situ sequencing of RNA barcodes. These data further demonstrates the use of BARseq to correlate gene expression and projections at cellular resolution with high throughput, and the use of BARseq to map projections of Cre-labeled subpopulation of neurons. These datasets Also contain two single-cell RNAseq datasets. One single-cell RNAseq dataset identified four Intratelencephalic neuron subtypes in mouse auditory cortex. A second single-cell RNAseq dataset compared endogenous gene expression in barcoded vs. non-barcoded neurons and found that information about endogenous gene expression can be successfully recovered from the barcoded neurons. Description of files in the current dataset: Dataset 2: BARseq and FISH data analysis.zip: processed data for XC75 and XC91 and script for reproducing all analyses in these two brains. script4types_590.mlx is a live script containing all analyses. workspace_4types_590.mat is the workspace after running through the script. The three other .mat files contain data from xc75, xc91, and clustering definition from xc9, xc14, xc28 (produced from analysis script for these three brains). Fezf2ercre BARseq: BARseq image data, projection barcode (barcodematrixXC92XC93.mat) and spike-in (spikes.mat) sequencing data, and processing script (script.mat) for processing and analyzing BARseq data in XC92. Both the original max projection images and processed/registered images are provided. dissection image***.zip: images of slices after dissection of brain areas for projection mapping. Slice summary - XC75 XC91 XC92.xlsx: list of correspondence between brain slices in the dissection images and slices in Allen Reference Atlas. XC91-234 images and processing script1.zip: Images and processing script for registering and processing XC91 BARseq data. Also requires XC91-234 images and processing script2.zip from dataset 4. Both original max projection images and registered/processed images are provided. scriptxc91.m process the images and produce the xc91 data matrix in "BARseq and FISH data analysis.zip".