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Experimental Overview



Sample GM11281 (3) | K562 (3)
Sample Post-QC GM11281 (3) | K562 (3)
Total Reads 90.10 K
Barcoded Reads 90.00 K
Fraction Barcoded Reads 1.00
Barcodes Identified 6
Reads per Barcode 15.00 K





Read Statistics

Read Count % of Barcoded Reads
Barcoded Reads 90,000 100.00
Trimmed Reads 89,243 99.16
Unmapped Reads 2,854 3.17
Mapped Reads 86,389 95.99
Uniquely Mapped Reads 80,310 89.23
Multimapped Reads 6,079 6.75
Total Exon Reads 75,473 83.86
Unique Exon Reads 70,426 78.25
Ambiguous Exon Reads 5,047 5.61
Total Intron Reads 2,889 3.21
Unique Intron Reads 2,567 2.85
Ambiguous Intron Reads 322 0.36
Intergenic Reads 1,948 2.16
Additional Information
Mitochondrial Reads 6,295 6.99
Ribosomal Reads 769 0.85


Reads by Sample Type

Reads per Barcode (Mean) Reads per Barcode (Median)
GM11281 15,000.00 15,000.00
K562 15,000.00 15,000.00


Genes by Sample Type

Genes per Barcode (Mean) Genes per Barcode (Median)
GM11281 85.00 85.00
ln(CPM10000) > 0.1 85.00 85.00
ln(CPM10000) > 1.0 85.00 85.00
K562 83.00 83.00
ln(CPM10000) > 0.1 83.00 83.00
ln(CPM10000) > 1.0 83.00 83.00


Ribosomal % by Sample Type

Ribosomal RNA % per Barcode (Mean) Ribosomal RNA % per per Barcode (Median)
GM11281 1.48 1.44
K562 0.46 0.27


Mitochondrial % by Sample Type

Mitochondrial % per Barcode (Mean) Mitochondrial % per per Barcode (Median)
GM11281 9.43 9.43
K562 6.32 6.94



Correlation Analysis


Heatmap



Boxplot

Min 1st Qu Median Mean 3rd Qu Max
GM11281 0.75 0.75 0.76 0.78 0.80 0.84
K562 0.83 0.84 0.86 0.87 0.90 0.93

Note: Correlation Analysis performed using the 85 genes identified for clustering.



Cluster Analysis


Principal Component Analysis (PCA)



Scree Plot

PC Variance % Variance by PCTOTAL % Variance by PC1-6 Correlation w/ Assigned Reads (r)
PC1 6.18 45.0 45.0 -0.82
PC2 4.55 24.4 24.4 0.44
PC3 3.50 14.4 14.4 0.04
PC4 2.92 10.0 10.0 -0.15
PC5 2.30 6.2 6.2 -0.33
PC6 0.00 0.0 0.0 0.77



Gene-wise Impact on Principal Components

Genes with Highest Impact on Principal Components 1-5
PC1 PC2 PC3 PC4 PC5
ENSG00000204287_HLA-DRA ENSG00000108298_RPL19 ENSG00000168028_RPSA ENSG00000198804_MT-CO1 ENSG00000174748_RPL15
ENSG00000019582_CD74 ENSG00000177600_RPLP2 ENSG00000096384_HSP90AB1 ENSG00000101608_MYL12A ENSG00000142937_RPS8
ENSG00000205542_TMSB4X ENSG00000137154_RPS6 ENSG00000198763_MT-ND2 ENSG00000100316_RPL3 ENSG00000181163_NPM1
ENSG00000005022_SLC25A5 ENSG00000198886_MT-ND4 ENSG00000184009_ACTG1 ENSG00000143947_RPS27A ENSG00000211459_MT-RNR1
ENSG00000111640_GAPDH ENSG00000198938_MT-CO3 ENSG00000185885_IFITM1 ENSG00000197958_RPL12 ENSG00000074800_ENO1
ENSG00000166710_B2M ENSG00000110700_RPS13 ENSG00000132475_H3F3B ENSG00000251562_MALAT1 ENSG00000210082_MT-RNR2
ENSG00000165678_GHITM ENSG00000137818_RPLP1 ENSG00000111669_TPI1 ENSG00000071082_RPL31 ENSG00000177954_RPS27
ENSG00000173660_UQCRH ENSG00000108654_DDX5 ENSG00000075624_ACTB ENSG00000149273_RPS3 ENSG00000166441_RPL27A
ENSG00000198786_MT-ND5 ENSG00000147604_RPL7 ENSG00000212907_MT-ND4L ENSG00000204628_RACK1 ENSG00000142534_RPS11
ENSG00000102144_PGK1 ENSG00000109971_HSPA8 ENSG00000084207_GSTP1 ENSG00000174748_RPL15 ENSG00000147403_RPL10



Uniform Manifold Approximation and Projection (UMAP)



Gene Expression Analysis


GM11281

mean expression *
GM11281 background logFC pval padj
ENSG00000111640_GAPDH 257.51 65.88 1.36 1.0e-01 1.8e-01
ENSG00000102144_PGK1 75.00 19.31 1.36 1.0e-01 1.8e-01
ENSG00000205542_TMSB4X 473.84 127.87 1.31 1.0e-01 1.8e-01
ENSG00000166710_B2M 387.39 117.00 1.20 1.0e-01 1.8e-01
ENSG00000134333_LDHA 184.81 61.90 1.09 1.0e-01 1.8e-01
ENSG00000198786_MT-ND5 135.04 53.29 0.93 1.0e-01 1.8e-01
ENSG00000075624_ACTB 479.22 191.96 0.91 2.0e-01 2.7e-01
ENSG00000210082_MT-RNR2 802.49 354.10 0.82 1.0e-01 1.8e-01
ENSG00000211459_MT-RNR1 152.42 74.08 0.72 1.0e-01 1.8e-01
ENSG00000184009_ACTG1 126.85 64.59 0.67 4.0e-01 4.1e-01


K562

mean expression *
K562 background logFC pval padj
ENSG00000165678_GHITM 152.21 21.22 1.97 1.0e-01 1.8e-01
ENSG00000117632_STMN1 270.80 40.12 1.91 1.0e-01 1.8e-01
ENSG00000213719_CLIC1 185.45 32.50 1.74 1.0e-01 1.8e-01
ENSG00000173660_UQCRH 99.26 17.90 1.71 1.0e-01 1.8e-01
ENSG00000087086_FTL 384.71 85.97 1.50 1.0e-01 1.8e-01
ENSG00000110955_ATP5F1B 146.65 39.12 1.32 1.0e-01 1.8e-01
ENSG00000005022_SLC25A5 111.35 30.73 1.29 1.0e-01 1.8e-01
ENSG00000173812_EIF1 173.75 50.46 1.24 1.0e-01 1.8e-01
ENSG00000164032_H2AFZ 140.00 41.69 1.21 1.0e-01 1.8e-01
ENSG00000143742_SRP9 92.84 29.76 1.14 1.0e-01 1.8e-01



&#42 Expression values are CPM normalized (scaled to 10000) and untransformed

Notes:

  1. The Correlation, Cluster and Gene Expression Analyses are performed post-QC. Samples that failed QC were dropped from the analysis.

  1. Samples were processed for QC by:

    Filtering for sample types within K562, GM11281.

    Removing cells with less than 10000 total read(s) or less than 300 gene(s).

    Removing genes with less than 100 total read(s) or expressed in fewer than 3 cell(s).

    Filtering for cells with 0-0.2 mitochondrial fraction and 0-0.1 intergenic fraction.

  2. Unless otherwise noted Cell counts were CPM normalized (scaled to 10000) and ln transformed.