Cell-type-specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1 (p.S858R) Schinzel Giedion Syndrome mice

DOI update for publication in JCMM:

The code and results below accompany the "Cell-type-specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1 (p.S858R) Schinzel Giedion Syndrome mice" manuscript.

The repository results include the following:

DEG: includes all differentially expressed genes from the cerebral cortex and brain snRNA-seq data.
ELISA: outputs from BCA and ELISA experiments used to quantify SETBP1 protein abundance.
alpaca: List of nodes in Setbp1 communities for cerebral cortex and kidney cell types
array_inputs: .txt files with the information needed to run array job scripts to construct PANDA networks and calculate TF activity with decoupleR.
diff_targeting: outputs from FEA on differentially targeted genes
seurat: intermediary files from snRNA-seq processing with Seurat as well as the input files to construct and final setbp1 target gene set used in this analysis (setbp1_targets.csv)
The repository data includes:

unprocessed: unprocessed input files used for TF-motif input construction and generation of the target gene set.

In addition, all data is publicly available on GEO (raw and processed FastQ files) and Zenodo (Docker images, input files, results, Seurat objects, and cell-type-specific PANDA regulatory networks for both tissues).

Cell-type-specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1 (p.S858R) Schinzel Giedion Syndrome mice

Network Data release:

The code and results below accompany the "Cell-type-specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1 (p.S858R) Schinzel Giedion Syndrome mice" manuscript.

The repository results include the following:

DEG: includes all differentially expressed genes from the cerebral cortex and brain snRNA-seq data.
ELISA: outputs from BCA and ELISA experiments used to quantify SETBP1 protein abundance.
alpaca: List of nodes in Setbp1 communities for cerebral cortex and kidney cell types
array_inputs: .txt files with the information needed to run array job scripts to construct PANDA networks and calculate TF activity with decoupleR.
diff_targeting: outputs from FEA on differentially targeted genes
seurat: intermediary files from snRNA-seq processing with Seurat as well as the input files to construct and final setbp1 target gene set used in this analysis (setbp1_targets.csv)
The repository data includes:

unprocessed: unprocessed input files used for TF-motif input construction and generation of the target gene set.

In addition, all data is publicly available on GEO (raw and processed FastQ files) and Zenodo (Docker images, input files, results, Seurat objects, and cell-type-specific PANDA regulatory networks for both tissues).

Setbp1 (p.S858R) variant shows cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome male mice

Data release:

The code and results below accompany the "Setbp1 (p.S858R) variant shows cell-type-specific expression and regulation in the cerebral cortex and kidney of atypical Schinzel Giedion Syndrome male mice" manuscript.

The repository results include the following:

DEG: includes all differentially expressed genes from the cerebral cortex and brain snRNA-seq data.
ELISA: outputs from BCA and ELISA experiments used to quantify SETBP1 protein abundance.
alpaca: List of nodes in Setbp1 communities for cerebral cortex and kidney cell types
array_inputs: .txt files with the information needed to run array job scripts to construct PANDA networks and calculate TF activity with decoupleR.
diff_targeting: outputs from FEA on differentially targeted genes
seurat: intermediary files from snRNA-seq processing with Seurat as well as the input files to construct and final setbp1 target gene set used in this analysis (setbp1_targets.csv)
The repository data includes:

unprocessed: unprocessed input files used for TF-motif input construction and generation of the target gene set.

In addition, all data is publicly available on GEO (raw and processed FastQ files) and Zenodo (Docker images, input files, results, and Seurat objects).

Setbp1 (p.S858R) variant shows cell-type-specific expression and regulation in cerebral cortex and kidney of atypical Schinzel Giedion Syndrome male mice

Initial release:

The code and results below accompany the "Setbp1 (p.S858R) variant shows cell-type-specific expression and regulation in the cerebral cortex and kidney of atypical Schinzel Giedion Syndrome male mice" manuscript.

The repository results include:

• DEG: includes all differentially expressed genes from cerebral cortex and brain snRNA-seq data.
• ELISA: outputs from BCA and ELISA experiments used to quantify SETBP1 protein abundance.
• alpaca: List of nodes contained in Setbp1 communities for cerebral cortex and kidney cell types
• array_inputs: .txt files with information needed to run array job scripts to construct PANDA networks and calculate TF activity with decoupleR.
• diff_targeting: outputs from FEA on differentially targeted genes
• seurat: intermediary files from snRNA-seq processing with Seurat as well as the input files to construct and final setbp1 target gene set used in this analysis (setbp1_targets.csv)

The repository data includes:

• unprocessed: unprocessed input files used for TF-motif input construction and generation of the target gene set.