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Series GSE100936 Query DataSets for GSE100936
Status Public on Dec 12, 2019
Title ChIP-seq for Gli1 and Gli2 in chondrosarcoma
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Excessive Hedgehog signaling in chondrocytes is sufficient to cause formation of enchondroma-like lesions in mice which can progress to chondrosarcoma. To elucidate potential mechanisms through which activation of Hedgehog signaling contributes to cartilage tumor formation, we used chromatin immunoprecipitation and next generation sequencing to identify Gli1 and Gli2 target genes in primary human chondrosarcoma. In silico analyses were conducted to identify and characterize Gli1 and Gli2 binding regions, including de novo motif analysis, co-localization with additional transcription factors, distance to transcriptional start site, conservation between human and mouse, and supervised and unsupervised analyses of biological pathways and processes. Our results profile putative unique and overlapping target genes of Gli1 and Gli2 in chondrosarcoma.
 
Overall design Cells were cultured from a primary chondrosarcoma obtained following surgery. Cells were divided into three groups and treated with Shh ligand to stimulate the Hedgehog signaling pathway. Following fixation, DNA was immunoprecipitated using antibodies against Gli1, Gli2, and IgG (negative control), and subjected to sequencing.
 
Contributor(s) Ali SA, Niu B, Cheah K, Alman B
Citation(s) 30695055
Submission date Jul 07, 2017
Last update date Jul 25, 2021
Contact name Benjamin Alman
Organization name Duke University
Street address 200 Trent Drive, Orange Zone 5th floor
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (3)
GSM2696858 Gli1
GSM2696859 Gli2
GSM2696860 IgG
Relations
BioProject PRJNA393452
SRA SRP111351

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Supplementary file Size Download File type/resource
GSE100936_RAW.tar 14.9 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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