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Series GSE70474 Query DataSets for GSE70474
Status Public on Sep 01, 2016
Title Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition [ATAC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Epithelial to mesenchymal transition (EMT) in cancer cells has been associated with metastasis, stemness and resistance to therapy. The reason why some tumors undergo EMT and other not might reflect intrinsic properties of their cell of origin, although this possibility is largely unexplored. By targeting the same oncogenic mutations to discrete skin compartments, we show cell type-specific chromatin and transcriptional states differentially prime tumors to EMT. Squamous cell carcinomas (SCCs) derived from intrafollicular epidermis (IFE) are generally well-differentiated, while hair follicle (HF) stem cell-derived SCCs frequently exhibit EMT, efficiently form secondary tumors, and possess increased metastatic potential. Transcriptional and epigenomic profiling revealed IFE and HF tumor-initiating cells possess distinct chromatin landscapes and gene regulatory networks associated with tumorigenesis and EMT that correlate with accessibility of key epithelial and EMT transcription factor binding sites. These findings highlight the importance of chromatin states and transcriptional priming in dictating tumor phenotypes and EMT.
 
Overall design Accessible chromatin regions were profiled using ATAC-seq, enriched peak regions were used to infer transcription factor binding sites.
 
Contributor(s) Latil ML, Beck B, Boumhadi S, Wang L, Brisebarre A, Yi R, Blanpain C
Citation(s) 27889319
Submission date Jul 02, 2015
Last update date May 15, 2019
Contact name C├ędric Blanpain
E-mail(s) cedric.blanpain@ulb.ac.be
Organization name ULB
Street address Route de Lennik 808
City Brussels
ZIP/Postal code 1070
Country Belgium
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (12)
GSM1782563 HF_normal_single-end
GSM1782564 HF_normal_paired-end
GSM1782565 IFE_normal_single-end
This SubSeries is part of SuperSeries:
GSE71621 Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition
Relations
BioProject PRJNA288786
SRA SRP060239

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE70474_ATAC_peaks.bed.gz 1.9 Mb (ftp)(http) BED
GSE70474_RAW.tar 7.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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