DOI: 10.5281/zenodo.14014437
title: Intermediate Data Files for Amygdala and Posterior Piriform Cortex RNA-ATAC Analysis

description: ### Description of Data Files

This dataset contains intermediate data files generated for the analysis of RNA and ATAC sequencing data from the amygdala and posterior piriform cortex. The files include ATAC-seq peak data, LOESS regression results, differential expression analysis, Gene Ontology (GO) analysis results, marker gene lists, and Seurat objects for further integrative analysis. Scripts and computational workflow can be found at https://github.com/karmaout/SOC_Multiomic_sequencing.




Filename
Description


PC_PR_Pyramidal_cfos_positive_atac.bed
BED file containing ATAC-seq peaks for cfos-positive VGLUT1a neurons in the PC under PR conditions.


BLA_PR_VGLUT1_cfos_positive_atac.bed
BED file with ATAC-seq peaks for cfos-positive VGLUT1 neurons in the BLA under PR conditions.


PC_PE_Pyramidal_cfos_negative_atac.bed
BED file for ATAC-seq peaks of cfos-negative VGLUT1a neurons in the PC under PE conditions.


PC_PR_loess_regression_data.csv
CSV file containing data for LOESS regression analysis in the PC under PR conditions.


BLA_cfos_percentages_raw_data.csv
Raw data of cfos expression percentages in different neuron populations in the BLA.


PC_PE_loess_regression_data.csv
LOESS regression data for the PC under PE conditions.


PC_neuron_cluster_markers.csv
CSV file listing marker genes for PC neuron clusters.


BLA_PE_VGLUT1_cfos_positive_atac.bed
BED file for ATAC-seq peaks of cfos-positive VGLUT1 neurons in the BLA under PE conditions.


BLA_PR_VGLUT1_cfos_negative_atac.bed
BED file for ATAC-seq peaks of cfos-negative VGLUT1 neurons in the BLA under PR conditions.


BLA_Subcluster_Differential_Expression_Results(with Fos).xlsx
Differential expression results for BLA subclusters with Fos gene.


PC_Aggregation.csv
Aggregated data for PC neurons, summarizing key statistics or metrics.


PC_Subcluster_Differential_Expression_Results_PC(with Fos).xlsx
Differential expression results for PC subclusters with Fos gene.


PC_cfos_percentages_raw_data.csv
Raw percentages of cfos expression in different PC neuron subclusters.


PC_PE_Pyramidal_cfos_positive_atac.bed
BED file for ATAC-seq peaks of cfos-positive Pyramidal neurons in the PC under PE conditions.


PC_PR_Pyramidal_cfos_negative_atac.bed
BED file for ATAC-seq peaks of cfos-negative Pyramidal neurons in the PC under PR conditions.


BLA_PR_loess_regression_data.csv
LOESS regression analysis data for the BLA under PR conditions.


BLA_GO_analysis_results_all_combined.xlsx
Combined Gene Ontology (GO) analysis results for BLA neuron populations.


PC_GO_analysis_results_all_combined.xlsx
Combined GO analysis results for PC neuron populations.


BLA_PR_anno_sorted_foldchange.txt
Annotated fold change data for BLA under PR conditions.


BLA_PE_anno_sorted_foldchange.txt
Annotated fold change data for BLA under PE conditions.


PC_PR_anno_sorted_foldchange.txt
Annotated fold change data for PC under PR conditions.


PC_PE_anno_sorted_foldchange.txt
Annotated fold change data for PC under PE conditions.


BLA_PE_loess_regression_data.csv
Data from LOESS regression analysis in the BLA under PE conditions.


BLA_PE_VGLUT1_cfos_negative_atac.bed
BED file for ATAC-seq peaks of cfos-negative VGLUT1 neurons in the BLA under PE conditions.


BLA_neuron_cluster_markers.csv
Marker genes for various neuron clusters in the BLA.


BLA_Aggregation.csv
Aggregated data for BLA neurons, summarizing key metrics or statistics.


BLA_neurons.rds
RDS file of the Seurat object for BLA neurons containing RNA and ATAC analysis.


PC_neurons.rds
RDS file of the Seurat object for PC neurons with integrated RNA and ATAC data.


BLA_matrix-scan.ft.txt
Matrix scan results for motif analysis in the BLA.


PC_coord_anno.txt
Annotated genomic coordinates for PC, used for integrative analysis.


BLA_coord_anno.txt
Annotated genomic coordinates for BLA.


PC_matrix-scan.ft.txt
Matrix scan results for motif analysis in the PC.