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Series GSE202315 Query DataSets for GSE202315
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
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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

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Supplementary file Size Download File type/resource
GSE202315_RAW.tar 3.4 Mb (http)(custom) TAR (of TBI)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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