Sample Information
| Sample ID | pbmc_1k_v3 |
|---|---|
| FASTQ Path | /liulab/galib/sc_CIDC/MAESTRO/test/tutorial/data/pbmc_1k_v3_fastqs/pbmc_1k_v3_S1_L001_R1_001.fastq.gz,/liulab/galib/sc_CIDC/MAESTRO/test/tutorial/data/pbmc_1k_v3_fastqs/pbmc_1k_v3_S1_L002_R1_001.fastq.gz |
| Species | GRCh38 |
| Platform | 10x-genomics |
Quality Control
Bulk level
Mappability
Read mappability and distribution of reads in coding regions (CDS) and intronic regions. In general, for human or mouse, uniquely mapped reads should account for more than 60% of all reads, and more reads should be distributed in exon regions than intron reads. La Manno et al (2018) found that for scRNA-seq, 15–25% of reads contained unspliced intronic sequences.
Reads quality
Phred quality score of scRNA-seq reads. The x-axis represents the position of reads from 5’ to 3’.
Reads nucleotide composition
Nucleotide frequency plot of scRNA-seq reads. The x-axis represents the position of reads from 5’ to 3’.
GC content
GC content distribution of scRNA-seq reads.
Gene body coverage
Reads distribution of gene body for scRNA-seq. Gene-body coverage evaluates sample read bias over 3’ or 5’ of the transcripts. For 10x-genomics, reads are supposed to be biased to 3' of the transcripts. For Smartseq2, reads are supposed to be distributed evenly over the transcripts.
Single-cell level
Cell filtering based on counts and covered genes
Cell filtering plot of scRNA-seq. The x-axis represents the number of unique reads/UMIs present in each cell, and the y-axis represents the number of genes covered in each cell.
Cell Clustering
Cell clustering based on gene expression
UMAP visualization of the clustering result. Colors represent different clusters with the cluster ID labeled.
Annotation
Celltype annotation
Celltype annotation based on DE genes
UMAP visualization of annotated clusters. Colors represent different cell types. The cell type information for each cluster is annotated using the expression level of marker genes.
Regulator annotation
Cluster-specific regulator identified by LISA
Driver transcription regulators identified based on cluster-specific genes. By default, the regulators are ranked by the enrichment score in each cluster.
| Cluster | Celltype Annotation | Transcription Factor | log10(LISA score) |
|---|---|---|---|
| 0 | CD4Tconv | BRD4 | 27.89 |
| 0 | CD4Tconv | GATA3 | ZEB1 | TCF3 | TFAP4 | TCF12 | LYL1 | ZBTB18 | SNAI1 | ASCL2 | 27.84 |
| 0 | CD4Tconv | EOMES | TBX21 | ZNF18 | TBX19 | 26.18 |
| 0 | CD4Tconv | CDK9 | 25.62 |
| 0 | CD4Tconv | CREBBP | 24.51 |
| 0 | CD4Tconv | ETS1 | ELF1 | FLI1 | ELF2 | ELK4 | ELK3 | NFAT5 | ETV6 | GABPA | ELK1 | ETV2 | ETS2 | 23.11 |
| 0 | CD4Tconv | IRF1 | STAT3 | STAT1 | IRF3 | STAT5B | PRDM1 | STAT4 | STAT5A | STAT2 | IRF2 | BCL6 | IRF4 | BCL11A | SPI1 | IRF8 | 22.28 |
| 0 | CD4Tconv | MYBL1 | MYB | 21.97 |
| 0 | CD4Tconv | MAF | MAFK | MAFG | MAFF | NRL | MAFB | 20.07 |
| 0 | CD4Tconv | NFKB1 | RELA | NFKB2 | REL | HIVEP1 | RELB | 20.02 |
| 1 | Mono/Macro | SPI1 | IRF1 | BCL6 | STAT2 | IRF8 | STAT1 | STAT3 | IRF2 | IRF3 | STAT5A | STAT5B | BCL11A | IRF4 | PRDM1 | SPIB | 64.45 |
| 1 | Mono/Macro | CEBPD | CEBPB | ATF4 | CEBPA | CEBPG | NFIL3 | DDIT3 | DBP | BATF | CEBPE | BATF3 | 61.9 |
| 1 | Mono/Macro | SMAD1 | 55.22 |
| 1 | Mono/Macro | JMJD1C | 48.51 |
| 1 | Mono/Macro | KMT2A | 46.75 |
| 1 | Mono/Macro | BRD4 | 45.7 |
| 1 | Mono/Macro | FLI1 | ELF1 | ETV6 | ETS2 | ELF2 | ELK3 | ELK4 | GABPA | NFAT5 | ELK1 | ELF3 | ETS1 | 42.01 |
| 1 | Mono/Macro | RUNX1 | CBFB | RUNX3 | RUNX2 | 40.68 |
| 1 | Mono/Macro | MED12 | 34.82 |
| 1 | Mono/Macro | CDK8 | 33.22 |
| 2 | CD4Tconv | TP53 | 25.26 |
| 2 | CD4Tconv | KAT2B | 25.09 |
| 2 | CD4Tconv | MYC | USF2 | MAX | MLX | MXI1 | USF1 | ARNTL | CLOCK | TFEB | TFE3 | BHLHE40 | ATF3 | 23.38 |
| 2 | CD4Tconv | BRD4 | 23.25 |
| 2 | CD4Tconv | ETS1 | ELF1 | ELK4 | FLI1 | ELF2 | ETV6 | NFAT5 | ELK1 | ELK3 | GABPA | ETS2 | ELF3 | ETV2 | 23.12 |
| 2 | CD4Tconv | EZH2 | 21.67 |
| 2 | CD4Tconv | MED1 | 21.23 |
| 2 | CD4Tconv | GTF2B | 20.15 |
| 2 | CD4Tconv | SNAPC1 | 19.76 |
| 2 | CD4Tconv | CDK9 | 19.5 |
| 3 | Mono/Macro | SPI1 | IRF1 | IRF8 | STAT2 | STAT3 | BCL6 | STAT1 | IRF2 | BCL11A | IRF3 | STAT5A | STAT5B | IRF4 | PRDM1 | SPIB | STAT4 | 65.81 |
| 3 | Mono/Macro | CEBPD | CEBPB | ATF4 | CEBPA | CEBPG | DDIT3 | NFIL3 | DBP | BATF3 | BATF | CEBPE | 57.27 |
| 3 | Mono/Macro | SMAD1 | 55.26 |
| 3 | Mono/Macro | JMJD1C | 49.94 |
| 3 | Mono/Macro | KMT2A | 48.9 |
| 3 | Mono/Macro | BRD4 | 46.47 |
| 3 | Mono/Macro | RUNX1 | RUNX3 | CBFB | RUNX2 | 39.76 |
| 3 | Mono/Macro | ELF1 | FLI1 | ETV6 | ETS2 | ELF2 | ELK4 | ELK3 | GABPA | NFAT5 | ELK1 | ETS1 | ETV2 | ELF3 | 38.31 |
| 3 | Mono/Macro | CDK8 | 35.46 |
| 3 | Mono/Macro | FOS | JUNB | JUND | JUN | FOSB | BACH1 | FOSL2 | NFE2L2 | NFE2 | BACH2 | FOSL1 | ZNF554 | 33.38 |
| 4 | B | FOXP1 | FOXO1 | FOXK1 | FOXO3 | FOXJ2 | FOXO4 | FOXM1 | 54.55 |
| 4 | B | BCL11A | IRF8 | SPIB | IRF1 | SPI1 | STAT3 | IRF3 | IRF2 | STAT2 | IRF4 | STAT1 | STAT5A | STAT5B | BCL6 | STAT4 | 47.88 |
| 4 | B | MEF2C | MEF2A | MEF2D | 42.35 |
| 4 | B | CREBBP | 40.28 |
| 4 | B | KMT2D | 34.09 |
| 4 | B | NCOR1 | 33.41 |
| 4 | B | SND1 | 32.89 |
| 4 | B | KMT2A | 32.86 |
| 4 | B | NCOR2 | 32.79 |
| 4 | B | REL | NFKB2 | RELA | NFKB1 | RELB | HIVEP1 | 31.58 |
| 5 | CD8T | GATA3 | ASCL2 | TCF3 | ZEB1 | TCF12 | TFAP4 | ZBTB18 | LYL1 | SNAI1 | TCF4 | 30.69 |
| 5 | CD8T | EOMES | TBX21 | ZNF18 | TBX19 | 26.85 |
| 5 | CD8T | MYBL1 | 19.75 |
| 5 | CD8T | IRF1 | STAT3 | PRDM1 | IRF3 | STAT4 | STAT1 | STAT5B | IRF2 | STAT5A | STAT2 | BCL6 | IRF8 | SPIB | IRF4 | BCL11A | SPI1 | 19.5 |
| 5 | CD8T | KMT2A | 16.67 |
| 5 | CD8T | CDK9 | 15.3 |
| 5 | CD8T | ETS1 | ELF1 | FLI1 | NFAT5 | ELF2 | ELK4 | ELK3 | ETV6 | GABPA | ETS2 | ELK1 | ETV2 | 14.04 |
| 5 | CD8T | REL | RELA | NFKB1 | NFKB2 | HIVEP1 | RELB | 13.55 |
| 5 | CD8T | RUNX3 | RUNX1 | RUNX2 | CBFB | 12.46 |
| 5 | CD8T | MAF | MAFG | MAFK | MAFF | NRL | MAFB | 12.37 |
| 6 | B | FOXP1 | FOXK1 | FOXO3 | FOXJ2 | FOXO1 | FOXO4 | FOXM1 | 34.4 |
| 6 | B | IRF8 | SPIB | BCL11A | IRF1 | IRF3 | SPI1 | STAT3 | IRF2 | STAT2 | STAT5B | STAT1 | IRF4 | PRDM1 | STAT5A | BCL6 | STAT4 | 30.19 |
| 6 | B | SND1 | 29.51 |
| 6 | B | NCOR2 | 29.37 |
| 6 | B | MEF2C | MEF2A | MEF2D | 28.85 |
| 6 | B | CD74 | 28.39 |
| 6 | B | CREBBP | 26.7 |
| 6 | B | REL | NFKB2 | RELB | NFKB1 | RELA | HIVEP1 | 22.99 |
| 6 | B | KMT2D | 22.78 |
| 6 | B | EBF1 | 22.47 |
| 7 | NK | ASCL2 | GATA3 | ZEB1 | TCF12 | TCF4 | TCF3 | ZBTB18 | SNAI1 | TFAP4 | 37.88 |
| 7 | NK | TBX21 | EOMES | ZNF18 | TBX19 | 34.73 |
| 7 | NK | MYBL1 | 26.13 |
| 7 | NK | KMT2A | 22.12 |
| 7 | NK | ETS1 | FLI1 | ELF1 | NFAT5 | ELK4 | ELF2 | ELK1 | GABPA | ETV6 | ETV2 | ELF3 | 19.28 |
| 7 | NK | RUNX3 | CBFB | RUNX1 | RUNX2 | 19.23 |
| 7 | NK | IRF1 | STAT4 | IRF3 | STAT3 | PRDM1 | IRF2 | IRF8 | STAT5A | STAT1 | STAT5B | STAT2 | BCL6 | 18.57 |
| 7 | NK | MED12 | 17.99 |
| 7 | NK | TCF7 | LEF1 | TCF7L2 | 17.98 |
| 7 | NK | NFIC | NFIA | HIC2 | 17.29 |
| 9 | Mono/Macro | SPI1 | IRF1 | STAT3 | BCL6 | IRF8 | STAT5A | STAT1 | IRF3 | STAT2 | BCL11A | IRF2 | STAT5B | SPIB | 44.2 |
| 9 | Mono/Macro | SMAD1 | 33.41 |
| 9 | Mono/Macro | KMT2A | 27.08 |
| 9 | Mono/Macro | RXRA | NR4A1 | RARA | NR4A2 | ESRRA | RXRB | VDR | NR4A3 | THRA | NR2C1 | PPARD | NR2F6 | RARG | 27.02 |
| 9 | Mono/Macro | RUNX3 | CBFB | RUNX1 | 26.42 |
| 9 | Mono/Macro | CEBPB | CEBPA | CEBPD | ATF4 | DBP | CEBPG | BATF3 | DDIT3 | NFIL3 | BATF | 26.33 |
| 9 | Mono/Macro | LMO2 | 26.07 |
| 9 | Mono/Macro | PML | 25.51 |
| 9 | Mono/Macro | JMJD1C | 25.29 |
| 9 | Mono/Macro | ELF1 | FLI1 | ELF2 | NFAT5 | ETS2 | ETV6 | ELK3 | GABPA | ELK1 | ELK4 | ETS1 | ELF3 | 24.75 |