 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 20, 2022 |
| Title |
Chemical, molecular, and single cell analysis reveal chondroitin sulfate proteoglycan aberrancy in fibrolamellar carcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Fibrolamellar carcinoma (FLC) is an aggressive liver cancer that predominantly afflicts adolescents and young adults. Patients with FLC are characterized by a heterozygous deletion on chromosome 19 that creates an oncogenic gene fusion, DNAJB1-PRKACA. The extracellular environment of FLC tumors is poorly characterized and may contribute to cancer progression, metastasis, and/or drug resistance. To bridge this knowledge gap, we propose to assess pathways relevant to proteoglycans, a major component of the extracellular matrix. We leveraged single-cell ATAC-seq to analyze the diversity of VCAN accessibility across different cell types.
|
| |
|
| Overall design |
Human primary tumor and adjacent nonmalignant liver samples were resected and flash frozen. We used single cell ATAC-seq to assess genome accessibility across three types of samples; non-malignant liver (n=2), primary fibrolamellar carcinoma tumor (n=2), and metastatic fibrolamellar carcinoma (n=2).
|
| |
|
| Contributor(s) |
Francisco AB, Li J, Farghli AR, Kanke M, Shui B, Munn PR, Grenier JK, Soloway PD, Wang Z, Reid LM, Liu J, Sethupathy P |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 05, 2022 |
| Last update date |
May 22, 2022 |
| Contact name |
Alaa Richard Farghli |
| E-mail(s) |
af547@cornell.edu
|
| Phone |
7189098209
|
| Organization name |
Cornell University
|
| Department |
Biomedical Sciences
|
| Lab |
Sethupathy
|
| Street address |
T7 006D Veterinary Research Tower, Box 17
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (6)
|
| GSM6108285 |
Liver, metastatic FLC, collagenase treated |
| GSM6108286 |
Liver, metastatic FLC, no treatment |
| GSM6108287 |
Liver, adjacent nonmalignant, collagenase treated |
|
| Relations |
| BioProject |
PRJNA835448 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE202315_RAW.tar |
3.4 Mb |
(http)(custom) |
TAR (of TBI) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...