Sample Editor (PDX or In Vitro Culture)

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NIH, National Cancer

Institute, Division of Cancer Treatment and Diagnosis (DCTD)

Sample

997537

175-T

Value Required

V1-organoid

Disease Body Location

Digestive/Gastrointestinal

COAD

10009951 - Adenocarcinoma - colon

Value Required

Organoid Culture

Media 6B/Colon 1A

PDX Fragment

FACS
Characterization

mMHC-, hHLA+, mCD9-, hCD9+, hCD90-, hEpCAM+, hCD24-

Growth Properties

Organoids

Proliferation Rate
in Complete Media

N/A

Sub-culture
Recommendations

1 Frozen Stock Vial can be used to generate: 4 wells in a 24-well plate

Culture Derivation

Derived from passage 0 PDX material.

Tumorigenic in
NSG Mice

Spheroid Growth

Spheroid Growth
Notes

N/A

Soft Agar Growth

Soft Agar
Growth Notes

N/A

Fibroblast qRT-PCR
C1 Corr

-0.32

Fibroblast qRT-PCR
C2 Corr

-0.40

Fibroblast qRT-PCR
Top Hits

KRT8,KRT18,EPCAM,KRT19,KRT20

Hide or show region

Images (if available)

In Vitro Images

View	Image Type	Notes	In Vitro Image
	Light Microscopy	Image of total well, 1 mm scale bar, Passage 14, 7 days in culture
	Light Microscopy	Magnified image, 500 micron scale bar, Passage 14, 7 days in culture
	Organoid H&E	10X image of embedded Patient-derived organoids
	Xenograft from In Vitro Culture	20X image of cell culture-derived xenograft

Genomic Analysis

External Genetic Analysis Data

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

2.0.2.51.0

Download Read1 FASTQ

Download Read2 FASTQ

2.0.2.51.0

Download Read1 FASTQ

Download Read2 FASTQ

2.0.2.4.0

Download RSEM (genes)

Download RSEM (isoforms)

2.0.2.4.0

OncoKB Gene Panel

View	Hugo Symbol	HGVS Protein Change	Variant Allele Frequency	Total Reads	Variant Class	Oncogenicity	Predicted Functional Effect	OncoKB Version
	ASXL1	p.G645Vfs*58	0.1227	163	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	ATM	p.K2811Sfs*46	0.4920	187	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	ATR	p.I774Yfs*5	0.4692	130	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	ATR	p.A14Pfs*35	0.1825	274	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	ATXN2	p.S590Rfs*58	0.1754	211	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	BRAF	p.V600E	0.5789	114	Missense_Mutation	Oncogenic	Gain-of-function	v3.14
	BRCA2	p.T3085Qfs*19	0.4726	201	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	CDKN1B	p.D63Rfs*62	0.6157	929	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	CREBBP	p.K1565Rfs*70	0.4979	486	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	EPHA7	p.X33_splice	0.5511	176	Splice_Site	Likely Oncogenic	Likely Loss-of-function	v3.14
	FAT1	p.X3402_splice	0.5411	207	Splice_Site	Likely Oncogenic	Likely Loss-of-function	v3.14
	FAT1	p.N126Kfs*3	0.4617	745	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	HNF1A	p.P291Qfs*51	0.5917	529	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	INHA	p.L189Cfs*2	0.1083	508	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	JAK1	p.P861Tfs*4	0.5529	416	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	KMT2C	p.K2797Rfs*26	0.4286	133	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	KMT2D	p.Q2109Afs*46	0.2844	225	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	MSH3	p.K383Rfs*32	0.9878	164	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	PHOX2B	p.G268Afs*41	0.4881	84	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	PIK3R1	p.R461*	0.4839	62	Nonsense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	PTEN	p.L57Wfs*42	0.4459	74	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	PTEN	p.K267Rfs*9	0.6077	130	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	RAD50	p.K722Rfs*14	0.5371	404	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	RECQL	p.V41Sfs*2	0.3418	509	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	RNF43	p.G659Vfs*41	0.5427	234	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	RNF43	p.R117Pfs*8	0.9785	186	Frame_Shift_Ins	Likely Oncogenic	Likely Loss-of-function	v3.14
	SESN2	p.Q229Rfs*18	0.5236	487	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	SOX9	p.510Lext49	0.4686	542	Nonstop_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	SPEN	p.A2105Lfs*33	0.4956	341	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	SPEN	p.P2461Hfs*15	0.4742	1029	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14
	TP53	p.R273C	0.5480	177	Missense_Mutation	Likely Oncogenic	Likely Loss-of-function	v3.14
	FANCL	p.Q99Rfs*17	0.4830	352	Frame_Shift_Del	Likely Oncogenic	Likely Loss-of-function	v3.14

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