GEO DataSets

(Submitter supplied) Organoid culture is important for maintenance of epithelial cell characteristics, stemness, and tumorigenic activity of biliary tract cancer initiating cells. To investigate whether organoid culture maintain cancer stem cell properties of biliary tract cancer initiating cells, we compared the gene expression changes between organoid culture and adherent culture.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21810

16 Samples

Download data: TXT

(Submitter supplied) To identify downstream genes involved in cholangiocarcinoma development by genetic manipulations of Kras, TGFbR2, and CDH1, we cultured the biliary organoid from the extrahepatic bile duct of Cre-negative LSL-KrasG12D;Tgfbr2flox/flox;CDH1flox/flox (KTC) mice, and induced gene recombination using a lentivirus expressing Cre-recombinase (Cre+ KTC organoid) or control lentivirus (Cre- KTC organoid). Then, we compared gene expression signatures between Cre- KTC organoid organoid and Cre+ KTC organoid.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

2 Samples

Download data: TXT

(Submitter supplied) Gene expression of mouse hepatoblasts (HBs) expressing IDH1 WT, IDH1 R132C, IDH2 WT, R172K and empty vector controls (N=2 cultures for each condition) grown on collagen-coated plates and IDH1 R132C and empty vector controls on uncoated plates were evaluated using Affymetrix Mouse 430Av2 DNA microarrays that were processed at the Dana-Farber Cancer Institute core facility (http://macf-web.dfci.harvard.edu/) using their standard protocol. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Datasets:

GDS5676 GDS5677

Platform:

GPL8321

14 Samples

Download data: CEL

Analysis of mutant IDH1 (R132C)-expressing hepatoblasts that were grown on uncoated plates to induce hepatocyte differentiation. IDH genes are frequently mutated in intrahepatic cholangiocarcinoma (IHCC). Results provide insight into the role of IDH1 in hepatocyte differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL8321

Series:

GSE57002

4 Samples

Download data: CEL

Analysis of hepatoblasts expressing mutant IDH1 (R132C) and mutant IDH2 (R172K) grown on collagen-coated plates. IDH genes are frequently mutated in intrahepatic cholangiocarcinoma (IHCC). Results provide insight into molecular pathways by which IDH mutations lead to tumor formation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 5 genotype/variation sets

Platform:

GPL8321

Series:

GSE57002

10 Samples

Download data: CEL

(Submitter supplied) Biliary tract cancer (BTC) has poor prognosis. The Notch receptor is aberrantly expressed in extrahepatic cholangiocarcinoma (eCCA). However, the role of Notch signaling in the initiation and progression of eCCA and gallbladder (GB) cancer remains unknown. We investigated the functional role of Notch signaling during tumorigenesis of the extrahepatic bile duct and GB. We demonstrated that simultaneous activation of the Kras–Akt and Notch pathways in EHBD and GB resulted in the formation of BilINs and biliary cancer in a mouse model. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

15 Samples

Download data: CEL, CHP

(Submitter supplied) Human IHCC cells were cultured with EM or DM and gene expression profiling was analyzed by microarray.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13915

1 Sample

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL18573 GPL24247

48 Samples

Download data

(Submitter supplied) To explore transcriptomic mechanisms underlying the proliferative, dedifferentiated phenotypes observed in ARID1A knockdown MMNK1 cell, We performed RNA-seq analysis on MMNK1 cells infected with sh-ARID1A versus sh-Scramble lentiviruses

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) To explore transcriptomic mechanisms underlying the cooperative effect in the proliferative phenotype, we harvest MEFs of different genotypes (KA, K, A, WT) recombined and un-recombined. We performed RNA-seq analysis on 5 recombined (Ad-CMV-Cre) cell lines of each genotypic conditions (WT, Arid1a L/L , Kras-LSL-G12D, and Kras-LSL-G12D; Arid1a L/L) as well as 2 or 3 un-recombined (Ad-CMV-GFP) or mock-infected MEF cell lines.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

30 Samples

Download data: TXT

(Submitter supplied) To explore mechanisms underlying the cooperative effect in the proliferative phenotype, we harvest MEFs of different genotypes (KA, K, A, WT) recombined and un-recombined.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) We have now developed an organoid-based model of gastric cancer from GAstric Neoplasia (GAN) mice, which express Wnt1 and the enzymes COX2 and microsomal prostaglandin E synthase 1 in the stomach. Both p53 knockout (GAN-p53KO) organoids and KRASG12V-expressing GAN-p53KO (GAN-KP) organoids were generated by genetic manipulation of GAN mouse–derived tumor (GAN-WT) organoids. To uncover the molecular mechanism underlying the intratumoral heterogeneity of GAN-KP tumors, we performed spatial transcriptomics analysis with the 10× Genomics Visium platform, which allows characterization of the spatial topography of gene expression.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

1 Sample

Download data: CSV, H5, JSON, PNG

(Submitter supplied) To develop a syngeneic mouse model of metastatic gastric cancer, we established the tumor organoids from gastric tumor arising in GAstric Neoplasia (GAN) mice (GAN-WT) which express Wnt1 and the PGE2 synthesis enzymes COX-2 and microsomal prostaglandin E synthase-1 (mPGES-1) in the stomach epithelium. Furthemore, GAN-WT organoids were genetically manupilated into p53 knockout organoids (GAN-p53KO) and KrasG12V-expressing GAN-p53KO organoids (GAN-KP).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21163

12 Samples

Download data: TXT

(Submitter supplied) The study of human liver cancer has been hampered by the lack of reliable models that faithfully recapitulate the physiopathology of the patient’s original tumour ex vivo. Here, we describe the first culture system to allow the establishment and long-term expansion of human primary liver cancer (PLC) organoids (called tumoroids) from the three most common PLC subtypes: Hepatocellular carcinoma (HCC), Cholangiocarcinoma (CC) and mixed HCC/CC tumours (CHC). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18460 GPL20301

59 Samples

Download data: TXT, VCF

(Submitter supplied) We revealed that concurrent activation of the Kras and canonical Wnt pathways resulted in formation of ICPN and BilIN, which could develop into biliary cancer. We found that c-Myc contributed to tumorigenesis, whereas Tgf-β pathway inhibited it.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

12 Samples

Download data: CEL

(Submitter supplied) Purpose: The aim of this study is to investigate mechanisms driving tumor-promoting mechanisms in cholangiocarcinoma while focusing on transitions from normal cholangiocytes to precancer lesions and from precancer lesion to invasive carcinoma. An original mouse model of intrahepatic cholangiocarcinoma was developed, based on induction of a KrasG12D mutation in cholangiocytes combined with chronic inflammation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: TSV, XLS

(Submitter supplied) The two oncogenes Myc and Kras cooperate to drive tumorigenesis and tumor suppressive pathways, to regulate the tumor microenvironment and to respond to immuno-therapies in different types of cancer. However, the interactions between Myc and Kras in cancer plasticity remain largely unknown. Primary liver cancer (PLC) comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC), two tumor subtypes which are morphologically and clinically different, and cell intrinsic molecular mechanisms that lead to the onset of HCC or ICC remain elusive. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TSV

(Submitter supplied) The two oncogenes Myc and Kras cooperate to drive tumorigenesis and tumor suppressive pathways, to regulate the tumor microenvironment and to respond to immuno-therapies in different types of cancer. However, the interactions between Myc and Kras in cancer plasticity remain largely unknown. Primary liver cancer (PLC) comprises hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC), two tumor subtypes which are morphologically and clinically different, and cell intrinsic molecular mechanisms that lead to the onset of HCC or ICC remain elusive. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: XLS

(Submitter supplied) The new concept of neoplastic lesion of biliary tree, Biliary intraepithelial neoplasia (BilIN) and intraductal papillary neoplasm of bile duct (IPNB), as a conunterpart of pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasm (IPMN), have been reported to be precancerous lesions in hilar and extrahepatic cholangiocarcinoma and arise from lining bile duct epithelium and peribiliary gland (PBG) under inflammation microenvironment in human. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21163

6 Samples

Download data: TXT