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Patient Specimen
Sample (PDX or In Vitro Culture)
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Patient ID
133474
Open Patient
Specimen ID
215-R2
Open Specimen
Sample ID
V3-organoid
Disease Body Location
Digestive/Gastrointestinal
OncoTree Code
IHCH
CTEP SDC Code
10004669 - Cholangiocar.- intra/extrahepatic
PDM Type
Organoid Culture
Required Media
Panc
Culture Origin
PDX Fragment
FACS
Characterization
mMHC-, hHLA+, mCD9-, hCD9+, hCD90-, hEpCAM+, CD24+
Growth Properties
Organoids
Proliferation Rate
in Complete Media
N/A
Sub-culture
Recommendations
1 Frozen Stock Vial can be used to generate: 24 wells in a 24-well plate
Culture Derivation
Derived from pooled passage 0 PDX material. Mouse cells were depleted from culture using magnetic beads labeled with anti-mCD9 and anti-mMHC antibodies.
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
0.00
Fibroblast qRT-PCR
C2 Corr
-0.11
Fibroblast qRT-PCR
Top Hits
KRT8, KRT18, KRT19,EpCAM,VIM
Images (if available)
In Vitro Images
View
Image Type
Notes
In Vitro Image
Light Microscopy
Image of total well, 1 mm scale bar, Passage 13, 7 days in culture
Light Microscopy
Magnified image, 500 micron scale bar, Passage 13, 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
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:
2.0.4.51.0
Whole Exome FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.4.51.0
RNASeq FASTQ (*.FASTQ.gz; for paired-end sequence, download both files)
Download Read1 FASTQ
Download Read2 FASTQ
Ver:
2.0.4.21.0
RNASeq Transcripts per Million (TPM; *.RSEM.genes.results and *.RSEM.isoforms.results tab-delimited text file)
Download RSEM (genes)
Download RSEM (isoforms)
Ver:
2.0.4.21.0
OncoKB Gene Panel
View
Hugo
Symbol
HGVS Protein
Change
Variant Allele
Frequency
Total
Reads
Variant
Class
Oncogenicity
Predicted
Functional Effect
OncoKB
Version
BRAF
p.V600E
0.4766
107
Missense_Mutation
Oncogenic
Gain-of-function
v4.27
BRIP1
p.R173C
0.6032
126
Missense_Mutation
Inconclusive
Inconclusive
v4.27
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