High-throughput mapping of long-range neuronal projection using in situ sequencing, Chen et al. dataset 1

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 1:
Helper scripts.zip: helper scripts needed to run all preprocessing and analysis scripts in MATLAB.
114-2 25 base validation.zip: Validation of BARseq by using the 1.5M barcode library.
BARseq vs retro tracing.zip: Comparison of BARseq and CTB tracing of contralateral projections (XC54)
Illumina vs SOLiD.zip: Comparison of Illumina and SOLiD sequencing in brain slices.
Analysis script-final1.zip: Analysis script, containing processed in situ barcode data and projection barcode data.
BARseq slice images.zip: images of dissection areas of XC9, XC28, and xc14 and corresponding areas in the Allen Reference Atlas.
XC9.zip: original and aligned images for XC9.
XC28-1.zip and XC28-2.zip: original and aligned images for XC28.
XC66.zip: original and aligned images for combined BARseq and FISH experiment.
Triple retrograde tracing.zip: images for the triple retrograde tracing experiment.