Sample Editor (PDX or In Vitro Culture)

Isolated from passage 0 PDX material. Sorted twice for EpCAM positive cells, grew the sample up resorted three times with EPCAM with a mCD9 exclusion. Final purification using cloning cylinders - all cells were pooled. Determined to be a tumor by qRT-PCR, FACS analysis, cell morphology and tumorigenicity

Tumorigenic in
NSG Mice

Spheroid Growth

Spheroid Growth
Notes

Soft Agar Growth

Soft Agar
Growth Notes

Fibroblast qRT-PCR
C1 Corr

-0.08

Fibroblast qRT-PCR
C2 Corr

-0.13

Fibroblast qRT-PCR
Top Hits

KRT18, KRT8, KRT19, KRT20, EPCAM, KIT, CD24, MUC1, KRT5, KRT15

Images (if available)

In Vitro Images

View	Image Type	Notes	In Vitro Image
	Light Microscopy	Phase contrast image [20X]: cells grown on plastic as adherent monolayer
	Spheroid Culture	Phase contrast image [20X]: Growth in StemPro media (no serum) results in growth as irregularly sized clusters
	Xenograft from In Vitro Culture	20x image of cell culture-derived xenograft; Diagnosis confirmed

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Genomic Analysis

External Genetic Analysis Data

A data file is available if a Download link is displayed:

2.0.1.50.0

1.2

1.2

Download RSEM (genes)

Download RSEM (isoforms)

Ver:

2.0.1.13.0

OncoKB Gene Panel

Hugo Symbol	HGVS Protein Change	Variant Allele Frequency	Total Reads	Variant Class	Oncogenicity	Predicted Functional Effect	OncoKB Version
AMER1	p.S501Efs*39	1.0000	68	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
APC	p.Q1477*	1.0000	419	Nonsense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
ATM	p.F858L	0.4925	467	Missense_Mutation	Likely Neutral	Likely Neutral	v3.14
KRAS	p.A146T	0.6271	59	Missense_Mutation	Oncogenic	Gain-of-function	v3.14
SMAD4	p.P356L	1.0000	111	Missense_Mutation	Likely Oncogenic	Unknown	v3.14
SOX9	p.E400*	0.2821	117	Nonsense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
TP53	p.R175H	1.0000	120	Missense_Mutation	Oncogenic	Loss-of-function	v3.14

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