1 Single cell expression data

Source:
High-throughput single-cell functional elucidation of neurodevelopmental disease-associated genes reveals convergent mechanisms altering neuronal differentiation, GEO accession: GSE142078.

Perturbations:
CRISPR knock-down of 14 autism spectrum disorder (ASD)–associated genes (3 gRNAs per gene) + 5 non-targeting gRNAs.

Cells:
Lund human mesencephalic (LUHMES) neural progenitor cell line.
Cells from 3 batches were merged together into 1 analysis. All cells have only a single type of gRNA readout. Quality control resulted in 8708 cells.

Genes:
Only genes detected in > 10% of cells were kept, resulted in 6213 genes.

Normalization:
Seurat “LogNormalize”: log(count per 10K + 1).
Batch effect, unique UMI count, library size, and mitochondria percentage were all corrected for. The corrected and scaled expression data were used as input for subsequent factor analysis.

2 Permutation

Cell labels in the expression data were permuted randomly so that they are no longer correlated with the knock-down conditions. Then GSFA was performed still using all conditions as guides. Factor-guide association as well as the LFSR of each gene were evaluated as usual.

In total, 10 random permutation rounds like this were conducted.

2.1 Factor ~ KO Beta PIP

2.2 Factor ~ KO Posterior Association

2.3 LFSR

Permutation 1, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA
Permutation 2, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA
Permutation 3, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA
Permutation 4, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA
Permutation 5, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA
Permutation 6, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA
Permutation 7, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA
Permutation 8, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA
Permutation 9, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA
Permutation 10, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8 CTNND2 DYRK1A HDAC5
Num_genes 0 0 0 0 0 0 0 0
KO MECP2 MYT1L Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 0 0 0 0 0 NA