Sample Information
| Sample ID | atac_pbmc_500_nextgem |
|---|---|
| Fragment Path | /liulab/galib/sc_CIDC/MAESTRO/test/tutorial/data/atac_pbmc_500_nextgem_fastqs |
| Species | GRCh38 |
| Platform | 10x-genomics |
Quality Control
Bulk level
Fragment size distribution
Fragment size distribution for 1% reads sampled from scATAC-seq. Only fragments with insert size less than 1,000 are considered. Y-axis represents the number of fragments. The fragment size distribution should show a periodicity of approximately 200bp due to nucleosome protection of the chromatin to transposase cutting.
Single-cell level
Cell filtering based on valid fragments and FRIP
Cell filtering plot of scATAC-seq. The x-axis represents the number of unique reads present in each cell, and the y-axis represents the fraction of reads in promoter regions (defined as 2kb up/downstream of TSS).
Cell Clustering
Cell clustering based on peaks
UMAP visualization of the clustering result. Colors represent different clusters with the cluster ID labeled.
Annotation
Celltype annotation
Celltype annotation based on RP and DE genes
UMAP visualization of annotated clusters. Colors represent different cell types. The cell type information for each cluster is annotated using the regulatory potential of marker genes.
Regulator annotation
Cluster-specific regulator identified by GIGGLE
Driver transcription regulators identified based on cluster-specific peaks. By default, the regulators are ranked by the enrichment score in each cluster.
| Cluster | Celltype Annotation | Transcription Factor | log10(Giggle score) |
|---|---|---|---|
| 0 | NK | ZNF18 | EOMES | TBX21 | TBX19 | 3.35 |
| 0 | NK | POLR2A | 3.34 |
| 0 | NK | GATA3 | ZBTB18 | TCF3 | TFAP4 | SNAI1 | ZEB1 | TCF12 | ASCL2 | LYL1 | MESP1 | NEUROD2 | TCF4 | NEUROG2 | BHLHA15 | SNAI2 | GATA1 | GATA2 | GATA6 | GATA5 | 3.29 |
| 0 | NK | KMT2A | 3.25 |
| 0 | NK | CREBBP | 3.24 |
| 0 | NK | EP300 | 3.24 |
| 0 | NK | TP53 | TP73 | 3.23 |
| 0 | NK | MYBL1 | MYB | 3.23 |
| 0 | NK | FOXP3 | 3.23 |
| 0 | NK | RUNX3 | RUNX1 | CBFB | RUNX2 | 3.22 |
| 1 | Neutrophils | POLR2A | 3.42 |
| 1 | Neutrophils | IRF1 | STAT3 | STAT2 | SPI1 | BCL6 | IRF2 | BCL11A | STAT1 | IRF3 | STAT5A | IRF8 | SPIB | STAT5B | IRF4 | PRDM1 | STAT4 | 3.39 |
| 1 | Neutrophils | KMT2A | 3.36 |
| 1 | Neutrophils | FOS | JUNB | FOSB | JUND | JUN | FOSL2 | NFE2L2 | NFE2 | BACH1 | FOSL1 | ZNF554 | BACH2 | 3.29 |
| 1 | Neutrophils | SP1 | EGR1 | KLF16 | SP4 | KLF13 | KLF6 | SP2 | KLF3 | KLF4 | KLF9 | EGR2 | SP3 | ZNF148 | ZBTB17 | ZNF281 | KLF5 | KLF1 | KLF12 | EGR4 | TBX1 | 3.28 |
| 1 | Neutrophils | NR4A1 | ESRRA | RARA | NR4A2 | RXRA | RARG | PPARD | NR4A3 | RXRB | PPARA | THRA | VDR | NR2F6 | NR1H3 | ESR2 | NR2C1 | ESR1 | RXRG | NR1I3 | NR1I2 | PPARG | 3.28 |
| 1 | Neutrophils | ZNF18 | EOMES | TBX21 | TBX19 | 3.28 |
| 1 | Neutrophils | RUNX1 | CBFB | RUNX3 | RUNX2 | 3.26 |
| 1 | Neutrophils | EP300 | 3.26 |
| 1 | Neutrophils | BHLHE40 | TFEB | ATF3 | MXI1 | ARNTL | TFE3 | MAX | HEY1 | USF1 | HES5 | MYC | HES7 | CLOCK | USF2 | MLX | MITF | HES1 | CREB3L1 | 3.24 |
| 2 | Treg | POLR2A | 3.29 |
| 2 | Treg | BRD4 | 3.27 |
| 2 | Treg | RAG2 | 3.27 |
| 2 | Treg | ZNF18 | EOMES | TBX21 | TBX19 | 3.26 |
| 2 | Treg | MBD3 | 3.25 |
| 2 | Treg | NRL | MAFF | MAFG | MAFK | MAF | MAFB | 3.24 |
| 2 | Treg | CREBBP | 3.24 |
| 2 | Treg | TET2 | 3.23 |
| 2 | Treg | CDK9 | 3.22 |
| 2 | Treg | EP300 | 3.22 |
| 3 | Mono/Macro | IRF1 | STAT3 | STAT2 | SPI1 | STAT1 | BCL6 | IRF2 | IRF3 | BCL11A | STAT5A | IRF4 | IRF8 | PRDM1 | STAT4 | STAT5B | SPIB | 3.42 |
| 3 | Mono/Macro | ZNF18 | TBX21 | EOMES | TBX19 | 3.34 |
| 3 | Mono/Macro | BRD4 | 3.31 |
| 3 | Mono/Macro | NR4A1 | NR4A2 | RARA | ESRRA | RARG | RXRA | PPARD | VDR | NR4A3 | THRA | RXRB | PPARA | NR2F6 | NR1H3 | ESR2 | NR2C1 | ESR1 | RXRG | NR1I3 | NR1I2 | PPARG | 3.27 |
| 3 | Mono/Macro | KMT2A | 3.25 |
| 3 | Mono/Macro | POLR2A | 3.24 |
| 3 | Mono/Macro | DPF2 | 3.22 |
| 3 | Mono/Macro | PML | 3.22 |
| 3 | Mono/Macro | GLI1 | 3.22 |
| 3 | Mono/Macro | DBP | DDIT3 | CEBPD | CEBPA | CEBPG | ATF4 | NFIL3 | CEBPB | BATF3 | CEBPE | BATF | HLF | 3.21 |
| 4 | CD4Tconv | POLR2A | 3.54 |
| 4 | CD4Tconv | EGR1 | SP1 | KLF13 | KLF9 | KLF16 | KLF6 | SP2 | SP4 | EGR2 | KLF12 | SP3 | ZBTB17 | KLF3 | ZNF281 | KLF4 | ZNF148 | EGR4 | KLF5 | KLF1 | TBX1 | 3.51 |
| 4 | CD4Tconv | BRD4 | 3.51 |
| 4 | CD4Tconv | ZNF18 | TBX21 | EOMES | TBX19 | 3.51 |
| 4 | CD4Tconv | NFATC3 | ZNF384 | NFATC1 | NFATC2 | NFATC4 | 3.51 |
| 4 | CD4Tconv | RUNX1 | RUNX3 | CBFB | RUNX2 | 3.51 |
| 4 | CD4Tconv | CHD2 | 3.51 |
| 4 | CD4Tconv | MED1 | 3.49 |
| 4 | CD4Tconv | ZNF143 | ZNF76 | THAP11 | 3.49 |
| 4 | CD4Tconv | BHLHE40 | ARNTL | MXI1 | HES7 | ATF3 | TFE3 | HES5 | TFEB | HEY1 | USF1 | MAX | MLX | MYC | CLOCK | USF2 | HES1 | CREB3L1 | MITF | 3.49 |
| 5 | B | LYL1 | ZBTB18 | ZEB1 | TFAP4 | TCF3 | SNAI1 | ASCL2 | TCF4 | TCF12 | MESP1 | BHLHA15 | NEUROD2 | NEUROG2 | GATA3 | SNAI2 | GATA1 | GATA2 | GATA5 | 3.33 |
| 5 | B | CD74 | 3.31 |
| 5 | B | KMT2A | 3.3 |
| 5 | B | SMARCA4 | 3.27 |
| 5 | B | POLR2A | 3.27 |
| 5 | B | CREBBP | 3.26 |
| 5 | B | IRF1 | STAT3 | BCL11A | STAT2 | IRF3 | BCL6 | STAT1 | IRF2 | IRF4 | STAT4 | SPI1 | STAT5A | IRF8 | SPIB | STAT5B | PRDM1 | 3.26 |
| 5 | B | NCOR2 | 3.26 |
| 5 | B | FOXO3 | FOXJ2 | FOXO6 | FOXO1 | FOXA3 | FOXP1 | FOXM1 | FOXO4 | FOXK1 | FOXD1 | FOXF1 | 3.26 |
| 5 | B | BCOR | 3.25 |
Gene Track
Gene track plot for each cluster
Gene track plot for each cluster. Here, CD3D nad MS4A1 are displayed as markers of T cells and B cells, respectively.
