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Patient ID
128128
Open Patient
Specimen ID
338-R
Open Specimen
Sample ID
J1-PDC
Disease Body Location
Skin
OncoTree Code
MEL
CTEP SDC Code
10053571 - Melanoma
PDM Type
PDC: Mixed Tumor Culture
Required Media
Complete DMEM/F12
Culture Origin
PDX Fragment
FACS
Characterization
mMHC-, hHLA+; mCD9-, hCD9+; hEpCAM-, hCD90-; hCD24-
Growth Properties
Adherent Monolayer
Proliferation Rate
in Complete Media
85 hrs
Sub-culture
Recommendations
Split ratio: 1 : 5. Grows as Loosely Attached Cells.
Culture Derivation
Isolated from passage 0 PDX material. Sorted three times for hCD9 positive cells. Determined to be a tumor by FACS analysis, QRT-PCR, cell morphology and positive tumorigenicity test
Tumorigenic in
NSG Mice
Yes
No
Spheroid Growth
Yes
No
Spheroid Growth
Notes
Grows as loose clusters
Soft Agar Growth
Yes
No
Soft Agar
Growth Notes
Fibroblast qRT-PCR
C1 Corr
0.23
Fibroblast qRT-PCR
C2 Corr
0.22
Fibroblast qRT-PCR
Top Hits
CD45,EPCAM,KRT19,FN1,KRT5
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
20x magnification
Spheroid Culture
20x magnification
Xenograft from In Vitro Culture
20x image of cell culture-derived xenograft
Export
Genomic Analysis
External Genetic Analysis Data
A data file is available if a Download link is displayed:
Somatic Mutations Associated with Cancer (*.vcf and *.maf)
Whole Exome Sequencing (*.vcf)
Download
Ver:
2.0.1.51.0
Whole Exome FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.1.51.0
RNASeq FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.1.4.0
RNASeq Transcripts per Million (TPM; *.RSEM.genes.results and *.RSEM.isoforms.results tab-delimited text file)
Download RSEM (genes)
Download RSEM (isoforms)
Ver:
2.0.1.4.0
OncoKB Gene Panel
View
Hugo
Symbol
HGVS Protein
Change
Variant Allele
Frequency
Total
Reads
Variant
Class
Oncogenicity
Predicted
Functional Effect
OncoKB
Version
BRAF
p.V600K
0.6848
92
Missense_Mutation
Oncogenic
Gain-of-function
v3.14
PPP6C
p.T120Nfs*32
0.3936
94
Frame_Shift_Del
Likely Oncogenic
Likely Loss-of-function
v3.14
SMARCA4
p.G1232S
0.4929
420
Missense_Mutation
Likely Oncogenic
Likely Loss-of-function
v3.14
Export
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