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Series GSE195661 Query DataSets for GSE195661
Status Public on Oct 13, 2022
Title Spatial transcriptomics reveal unnresolved wound repair as potential driver of PFA Ependymoma progression
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Childhood brain tumor ependymoma remains incurable in approximately 50 percent of cases. No oncogenic mechanism has been firmly established for the commonest ependymoma variant posterior fossa subgroup A (PFA), impeding clinical advances. Uncovering how heterogeneous cell types within the tumor microenvironment interact is crucial to a complete understanding of PFA disease progression. The underlying cellular components of the PFA tumor microenvironment have been revealed by single cell transcriptomics, identifying divergent epithelial differentiation and EMT lineages. Here we utilize spatial transcriptomics (Visium) of 14 PFA samples to chart neoplastic and immune cell architecture and identify novel biological processes.
Overall design spatial transcriptomics (Visium) of 14 PFA samples
Contributor(s) Fu R, Norris G, Willard N, Foreman N, Donson A
Citation(s) 36215273
Submission date Jan 28, 2022
Last update date Oct 19, 2022
Contact name RUI FU
Organization name New York Genome Center
Department Computational Biology
Street address 101 6th Ave
State/province NY
ZIP/Postal code 10013
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (14)
GSM5844711 surgically resected tumor 459
GSM5844712 surgically resected tumor 723
GSM5844713 surgically resected tumor 727
BioProject PRJNA801698

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

Supplementary file Size Download File type/resource
GSE195661_RAW.tar 4.0 Gb (http)(custom) TAR (of H5, TIFF)
GSE195661_cell_metadata.tsv.gz 1.9 Mb (ftp)(http) TSV
GSE195661_spaceranger_spatial_dirs.tar.gz 125.3 Mb (ftp)(http) TAR
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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