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GSE133509

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Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development

Organism: Homo sapiens
Platform: GPL24676
Samples: 14
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jun 28 2019
Last Updated: Jul 14 2020
Status: Public on Dec 10 2019
Contact: Gene,,Yeo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA551658 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP212301

Summary

Many current cellular models aimed to elucidate cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a new cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that capture authentic cancer pathobiology. Orthotopic engraftment of the neural progenitor cells derived from hiPSCs introduced with tumor-associated genetic driver mutations revealed by The Cancer Genome Atlas project for glioblastoma (GBM) results in formation of brain tumors. As observed in GBM patient samples, these models harbor inter-tumor heterogeneity resembling different GBM molecular subtypes, and intra-tumor heterogeneity. Further, re-engraftment of these tumor cells generate tumors with features characteristic of patient samples and present mutation-dependent patterns of tumor evolution. Thus, these cancer avatar models provide a platform for a comprehensive longitudinal assessment of human tumor development as governed by molecular subtype mutations.

Overall Design

Analyses on inter- and intra-tumor heterogeneity of different glioblastoma derived from differentially engineered isogenic human induced pluripotent stem cells.

Analysis (1 step)

View Data Processing
Processing steps for GSE133509
  1. alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 2.1.1)

Supplementary Files (1)

GSE133509_RAW.tar Download
GEO Samples (14)
GSM3910556 GSM3910557 GSM3910558 GSM3910559 GSM3910560 GSM3910561 GSM3910562 GSM3910563 GSM3910564 GSM3910565 GSM3910566 GSM3910567 GSM3910568 GSM3910569

Dataset Citations (1)

Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.
PMID 31992716 · 2020 · Nature communications
Tomoyuki Koga, Isaac A Chaim, Jorge A Benitez, Sebastian Markmiller, Alison D Parisian, Robert F Hevner, Kristen M Turner, Florian M Hessenauer, Matteo D'Antonio, Nam-Phuong D Nguyen, Shahram Saberi, Jianhui Ma, Shunichiro Miki, Antonia D Boyer, John Ravits, Kelly A Frazer, Vineet Bafna, Clark C Chen, Paul S Mischel, Gene W Yeo, Frank B Furnari

SRA Experiments (14) and Runs (14)

Total: 83983 MB
SRX6375055 SRP212301 RNA-Seq PAIRED
GSM3910556: P-S1; Homo sapiens; RNA-Seq
Sample: SRS5035847
BioProject: PRJNA551658
BioSample: SAMN12161946
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: PTEN KO / NF1 KO
passage: 5-10
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611927 184957881 27928640031 5169.59 3_5_1C_TK_possorted_genome_bam.bam, SRR9611927, SRR9611927.sralite SRA
SRX6375056 SRP212301 RNA-Seq PAIRED
GSM3910557: P-T2.1; Homo sapiens; RNA-Seq
Sample: SRS5035848
BioProject: PRJNA551658
BioSample: SAMN12161969
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: PTEN KO / NF1 KO
passage: 0
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611928 173236379 26158693229 5045.16 17_1_1T_TK_possorted_genome_bam.bam, SRR9611928, SRR9611928.sralite SRA
SRX6375057 SRP212301 RNA-Seq PAIRED
GSM3910558: P-T2.2; Homo sapiens; RNA-Seq
Sample: SRS5035850
BioProject: PRJNA551658
BioSample: SAMN12161968
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: PTEN KO / NF1 KO
passage: 0
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611929 189096662 28553595962 5408.25 17_1_2T_TK_possorted_genome_bam.bam, SRR9611929, SRR9611929.sralite SRA
SRX6375058 SRP212301 RNA-Seq PAIRED
GSM3910559: P-T2.3; Homo sapiens; RNA-Seq
Sample: SRS5035849
BioProject: PRJNA551658
BioSample: SAMN12161967
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: PTEN KO / NF1 KO
passage: 0
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611930 239974056 36236082456 6862.0 17_1_3T_TK_possorted_genome_bam.bam, SRR9611930, SRR9611930.sralite SRA
SRX6375059 SRP212301 RNA-Seq PAIRED
GSM3910560: P-S2.1; Homo sapiens; RNA-Seq
Sample: SRS5035851
BioProject: PRJNA551658
BioSample: SAMN12161966
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: PTEN KO / NF1 KO
passage: 5-10
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611931 64477384 9736084984 1668.45 17_1_1C_TK_possorted_genome_bam.bam, SRR9611931, SRR9611931.sralite SRA
SRX6375060 SRP212301 RNA-Seq PAIRED
GSM3910561: P-S2.2; Homo sapiens; RNA-Seq
Sample: SRS5035852
BioProject: PRJNA551658
BioSample: SAMN12161965
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: PTEN KO / NF1 KO
passage: 5-10
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611932 64023104 9667488704 1639.38 17_1_2C_TK_possorted_genome_bam.bam, SRR9611932, SRR9611932.sralite SRA
SRX6375061 SRP212301 RNA-Seq PAIRED
GSM3910562: P-S2.3; Homo sapiens; RNA-Seq
Sample: SRS5035853
BioProject: PRJNA551658
BioSample: SAMN12161964
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: PTEN KO / NF1 KO
passage: 5-10
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611933 52259844 7891236444 1360.55 17_1_3C_TK_possorted_genome_bam.bam, SRR9611933, SRR9611933.sralite SRA
SRX6375062 SRP212301 RNA-Seq PAIRED
GSM3910563: T-S1; Homo sapiens; RNA-Seq
Sample: SRS5035854
BioProject: PRJNA551658
BioSample: SAMN12161963
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: TP53 KO / PDGFRA mut
passage: 5-10
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611934 412206035 62243111285 11186.37 3_7_1C_TK_possorted_genome_bam.bam, SRR9611934, SRR9611934.sralite SRA
SRX6375063 SRP212301 RNA-Seq PAIRED
GSM3910564: T-T2.1; Homo sapiens; RNA-Seq
Sample: SRS5035855
BioProject: PRJNA551658
BioSample: SAMN12161961
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: TP53 KO / PDGFRA mut
passage: 0
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611935 63820366 9636875266 1780.45 17_2_1T_TK_possorted_genome_bam.bam, SRR9611935, SRR9611935.sralite SRA
SRX6375064 SRP212301 RNA-Seq PAIRED
GSM3910565: T-T2.2; Homo sapiens; RNA-Seq
Sample: SRS5035856
BioProject: PRJNA551658
BioSample: SAMN12161960
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: TP53 KO / PDGFRA mut
passage: 0
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611936 69628870 10513959370 1974.64 17_2_2T_TK_possorted_genome_bam.bam, SRR9611936, SRR9611936.sralite SRA
SRX6375065 SRP212301 RNA-Seq PAIRED
GSM3910566: T-T2.3; Homo sapiens; RNA-Seq
Sample: SRS5035857
BioProject: PRJNA551658
BioSample: SAMN12161959
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: TP53 KO / PDGFRA mut
passage: 0
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611937 136281851 20578559501 3812.59 17_2_3T_TK_possorted_genome_bam.bam, SRR9611937, SRR9611937.sralite SRA
SRX6375066 SRP212301 RNA-Seq PAIRED
GSM3910567: T-S2.1; Homo sapiens; RNA-Seq
Sample: SRS5035858
BioProject: PRJNA551658
BioSample: SAMN12161957
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: TP53 KO / PDGFRA mut
passage: 5-10
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611938 538126554 81257109654 14231.37 17_2_1C_TK_possorted_genome_bam.bam, SRR9611938, SRR9611938.sralite SRA
SRX6375067 SRP212301 RNA-Seq PAIRED
GSM3910568: T-S2.2; Homo sapiens; RNA-Seq
Sample: SRS5035859
BioProject: PRJNA551658
BioSample: SAMN12161956
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: TP53 KO / PDGFRA mut
passage: 5-10
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611939 445536850 67276064350 11556.69 17_2_2C_TK_possorted_genome_bam.bam, SRR9611939, SRR9611939.sralite SRA
SRX6375068 SRP212301 RNA-Seq PAIRED
GSM3910569: T-S2.3; Homo sapiens; RNA-Seq
Sample: SRS5035860
BioProject: PRJNA551658
BioSample: SAMN12161955
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: induced glioblastoma cells
biomaterial_provider: Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25430&Product=CC
original cell line: CVB - iPSC (Coriell GM25430)
genotype: TP53 KO / PDGFRA mut
passage: 5-10
Original files (1)
induced glioblastoma cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9611940 469067065 70829126815 12287.55 17_2_3C_TK_possorted_genome_bam.bam, SRR9611940, SRR9611940.sralite SRA

Linked Publications (1)

Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.
Nature communications · 2020

Data Files (14)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 17_1_1C_TK_possorted_genome_bam.bam RNA-Seq 1.6 GB link
— 17_1_1T_TK_possorted_genome_bam.bam RNA-Seq 4.9 GB link
— 17_1_2C_TK_possorted_genome_bam.bam RNA-Seq 1.6 GB link
— 17_1_2T_TK_possorted_genome_bam.bam RNA-Seq 5.3 GB link
— 17_1_3C_TK_possorted_genome_bam.bam RNA-Seq 1.3 GB link
— 17_1_3T_TK_possorted_genome_bam.bam RNA-Seq 6.7 GB link
— 17_2_1C_TK_possorted_genome_bam.bam RNA-Seq 13.9 GB link
— 17_2_1T_TK_possorted_genome_bam.bam RNA-Seq 1.7 GB link
— 17_2_2C_TK_possorted_genome_bam.bam RNA-Seq 11.3 GB link
— 17_2_2T_TK_possorted_genome_bam.bam RNA-Seq 1.9 GB link
— 17_2_3C_TK_possorted_genome_bam.bam RNA-Seq 12.0 GB link
— 17_2_3T_TK_possorted_genome_bam.bam RNA-Seq 3.7 GB link
— 3_5_1C_TK_possorted_genome_bam.bam RNA-Seq 5.0 GB link
— 3_7_1C_TK_possorted_genome_bam.bam RNA-Seq 10.9 GB link