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Series GSE133785 Query DataSets for GSE133785
Status Public on Jul 30, 2019
Title Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis [ATAC-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Langerhans cell histiocytosis (LCH) is a rare neoplasm predominantly affecting children. It occupies a characteristic hybrid position between cancers and inflammatory diseases, which makes it an attractive model for studying cancer development. To explore the molecular mecha-nisms underlying the pathophysiology of LCH and its characteristic clinical heterogeneity, we investi-gated the transcriptomic and epigenomic diversity in primary LCH lesions. Using single-cell RNA se-quencing, we identified multiple recurrent types of LCH cells within these biopsies, including putative LCH progenitor cells and several subsets of differentiated LCH cells. We confirmed the presence of pro-liferative LCH cells in all analysed biopsies using immunohistochemistry, and we defined the epigenomic and gene-regulatory basis of the different LCH cell subsets using chromatin profiling. In summary, our single-cell analysis of LCH uncovered an unexpected degree of cellular, transcriptomic, and epigenomic heterogeneity among LCH cells, reflecting complex developmental hierarchies in LCH lesions.
 
Overall design ATAC-seq analysis of three FACS-enriched LCH cell subsets (in duplicate) from a biopsy = 6 datasets total.
**The submitter declares that the raw sequence data have been deposited at the European Genome-Phenome Archive (EGA) to protect patient privacy.**
 
Contributor(s) Halbritter F, Farlik M, Schwentner R, Jug G, Fortelny N, Schnöller T, Pisa H, Schuster L, Reinprecht A, Czech T, Gojo J, Holter W, Minkov M, Bauer W, Simonitsch-Klupp I, Bock C, Hutter C
Citation(s) 31345789
Submission date Jul 03, 2019
Last update date Jul 30, 2019
Contact name Christoph Bock
E-mail(s) cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (6)
GSM3927308 LCH_S1_3 [ATAC-seq]
GSM3927309 LCH_S1_4 [ATAC-seq]
GSM3927310 LCH_S11_3 [ATAC-seq]
This SubSeries is part of SuperSeries:
GSE133706 Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis
Relations
BioProject PRJNA552543

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
GSE133785_RAW.tar 847.0 Mb (http)(custom) TAR (of BW, NARROWPEAK)
GSE133785_atac_peaks_geo.csv.gz 966.0 Kb (ftp)(http) CSV
Processed data provided as supplementary file
Processed data are available on Series record
Raw data not provided for this record

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