Mafe Senosain

PhD Candidate in Cancer Biology @ Vanderbilt University in the Massion Lab

  1. CyTOF
  2. RNA Seq
  3. WES
  4. Single cell RNA Seq
  5. MxIF from UC Davis
  6. Radiomics
  7. Clinical data

CyTOF

  1. General info: Mass Cytometry or CyTOF is a variation of flow cytometry in which antibodies are labeled with heavy metal ion tags rather than fluorochromes. Our antibody panel include the following protein markers:
Antigen Isotope Working conc (ug/ml) Dilution Vol in 100 ul rx Level Clone Source Catalog #
EpCAM 141-Pr   1:1600 0.0625 S 9C4 Fluidigm 3141006B
c caspase3 142-Nd   1:400 0.25 I D3E9 Fluidigm 3142004A
* TP53 143-Nd 50 1:200 0.25 I DO-7 Biolegend 645802
HLA-ABC 144-Nd   1:800 0.125 S W6/32 Fluidigm 3144017B
CD31 145-Nd   1:200 0.5 S WM59 Fluidigm 3145004B
Thioredoxin 146-Nd   1:800 0.125 I 2G11/TRX Fluidigm 3146016B
b-CAT 147-Sm   1:800 0.125 I D10A8 Fluidigm 3147005A
HER2 148Nd   1:400 0.25 S 29D8 Fluidigm 3148011A
p-STAT6 149-Sm   1:200 0.5 I 18/P-Stat6 Fluidigm 3149004A
p-stat5 150-Nd   1:200 0.5 I Y694 Fluidigm 3150005A
* TTF1 151-Eu 100 1:200 0.5 I D2E8 CST 12373
p-AKT 152-Sm   1:400 0.25 I D9E Fluidigm 3152005A
* ki67 153-Eu 100 1:200 0.5 I ki67 Biolegend 350523
CD45 154-Sm   1:800 0.125 S HI30 Fluidigm 3154001B
CD56/NCAM 155-Gd   1:100 1 S B159 Fluidigm 3155008B
Vimentin 156-Gd   1:800 0.125 I RV202 Fluidigm 3156023A
p-STAT3 158-Gd   1:200 0.5 I Y705 Fluidigm 3158005A
* CD4 159-Tb 100 1:400 0.25 S RPA T4 Biolegend 300502
* MDM2 160-Gd 100 1:200 0.5 I Polyclonal Abcam ab38618
* Cytokeratin 161-Dy 50 1:400 0.25 I C-11 Abcam ab7753
* MET 162-Dy 50 1:300 0.32 S L6E7 CST 8741
* TP63 163-Dy ? 1:200 0.5 I W15093A Biolegend 687202
CK7 164-Dy   1:400 0.25 I RCK105 Fluidigm 3164020A
* total EGFR 165-Ho 50 1:250 0.4 S AY13 Biolegend 352902
CD44 166-Er   1:800 0.125 S BJ18 Fluidigm 3166001B
p-ERK 167-Er   1:400 0.25 I D13.14.4E Fluidigm 3167005A
CD8 168-Er   1:200 0.5 S RPA-T8 Fluidigm 3168002B
CD24 169-Tm   1:200 0.5 S ML5 Fluidigm 3169004B
CD3e 170-Yb   1:400 0.25 S SP34-2 Fluidigm 3170007B
* CD11b 171-Yb 50 1:400 0.25 S ICRF44 Biolegend 301337
p-S6 172-Yb   1:400 0.5 I N7-548 Fluidigm 3172008A
HLA-DR 174-Yb   1:400 0.5 S L243 Fluidigm 3172008A
CD274/PDL1 175-Lu   1:800 0.125 S 29E.2A3 Fluidigm 3175017B
Histone H3 176-Yb   1:200 0.5 I D1H2 Fluidigm 3176016A

Table 1. Antibody panel for lung adenocarcinoma. * In-house conjugated antibodies. S = Surface, I = Intracellular

  1. Description of data files:
    1. Raw data: FCS files
      • 71 Patient samples
      • 20 (?) running controls (A549 + Ramos)
      • X validation cell lines
    2. Processed data: CSV files
      • CSV file with all patient data concatenated and annotation columns for cell types and sub cell types and ptID column
      • CSV file with all control data concatenated and ID column
      • CSV file with all validation cell lines concatenated and ID column
  2. Location:

RNA Seq

  1. General info: NGS transcriptomic data. This data set has been pre-processed by Shillin Zhao.
  2. Description of data files:
    1. Raw data: FASTQ files
      • 78 samples (X from fresh frozen tissue, Y from single cell suspension, Z patients with overlapping data)
    2. Processed data (align to Hg38): CSV files
      • Raw counts
      • FPKM normalized counts
  3. Location:

WES

  1. General info: Twist Whole Exome Sequencing data, NGS genomic data. This data set has been pre-processed by Shillin Zhao.
  2. Description of data files:
    1. Raw data: FASTQ files
      • 58 tumors and their matching normal tissue controls
    2. Processed data: MAF file
      • Mutation data for 58 patients
  3. Location:

Single cell RNA Seq

  1. General info: NGS single cell transcriptomic data. Platform used for library prep was 10X genomics 5’. This data set has been pre-processed by Shillin Zhao and VANTAGE.
  2. Description of data files:
    1. Raw data: FASTQ files
      • 16 samples of “Good” and “Poor” CANARY prognosis.
    2. Processed data:
      • 16 matrices with raw counts (rows are cells, columns are genes)
  3. Location:

MxIF from UC Davis

  1. General info: This data was acquired and processed by our MCL grant collaborators in UC Davis, Alexander Borowsky team.
    • Data for 93 patients with duplicates. 2 TMA blocks with 186 punches + controls.
    • Antibody panels
    • Panel 1 Panel 2    
      CD3 Lymphocytes CD3 Lymphocytes
      CD20 B cells CD68 Macrophages
      HLA-DR MHC-II CKs Epithelial cells
      FOX-P3 T regs PDL1 IC protein
      CKs Epithelial cells PD1 IC protein
      Ki67 Proliferation CD8 Cytotoxic T cells
  2. Description of data files:
    1. Raw data:
    2. Processed data:
  3. Location:

Radiomics

  1. General info: This data set is composed by the raw CT scans, the HealthMyne radiomic features, CANARY prognosis predictions and SILA scores. Khushbu Patel is the current person in charge.
  2. Description of data files:
    1. Raw data:
      • 92 CT scans
    2. Processed data: CSV files
      • HealthMyne radiomic features
      • CANARY + SILA scores
  3. Location: