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Patient Specimen
Sample (PDX or In Vitro Culture)
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Patient ID
119177
Open Patient
Specimen ID
322-R1
Open Specimen
Sample ID
V1-organoid
Disease Body Location
Musculoskeletal
OncoTree Code
SYNS
CTEP SDC Code
10042866 - Synovial sarcoma
PDM Type
Organoid Culture
Required Media
Media 6A
Culture Origin
PDX Fragment
FACS
Characterization
mMHC-, hHLA+, mCD9-, hCD9+, hCD90+, hEpCAM-, CD24-
Growth Properties
Aggregate Clusters
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 6 PDX material.
Tumorigenic in
NSG Mice
Yes
No
Spheroid Growth
Yes
No
Spheroid Growth
Notes
N/A
Soft Agar Growth
Yes
No
Soft Agar
Growth Notes
N/A
Fibroblast qRT-PCR
C1 Corr
0.75
Fibroblast qRT-PCR
C2 Corr
0.71
Fibroblast qRT-PCR
Top Hits
FN1,VIM,KRT8,KRT16,KRT18
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
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:
2.0.2.51.0
Whole Exome FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.2.51.0
RNASeq FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.2.21.0
RNASeq Transcripts per Million (TPM; *.RSEM.genes.results and *.RSEM.isoforms.results tab-delimited text file)
Download RSEM (genes)
Download RSEM (isoforms)
Ver:
2.0.2.21.0
OncoKB Gene Panel
View
Hugo
Symbol
HGVS Protein
Change
Variant Allele
Frequency
Total
Reads
Variant
Class
Oncogenicity
Predicted
Functional Effect
OncoKB
Version
BRCA2
p.Y42C
0.4831
89
Missense_Mutation
Likely Neutral
Likely Neutral
v4.11
TERT
p.H412Y
0.5122
123
Missense_Mutation
Likely Neutral
Likely Loss-of-function
v4.11
RNASEH2B
p.N305Kfs*2
0.5556
27
Frame_Shift_Ins
Likely Oncogenic
Likely Loss-of-function
v4.11
Export
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