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Series GSE117825 Query DataSets for GSE117825
Status Public on Jun 01, 2019
Title Amplicon of Single-Cell Genotyping of Transcriptomes
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Somatic cancer driver mutations may result in distinctly diverging phenotypic outputs. Thus, a common driver lesion may result in cancer subtypes with distinct clinical presentations and outcomes. The diverging phenotypic outputs of mutations result from the superimposition of the mutations with distinct progenitor cell populations that have differing lineage potential. However, our ability to test this hypothesis has been challenged by currently available tools. For example, flow cytometry is limited in its inability to resolve lineage commitment of early progenitors. Single-cell RNA sequencing (scRNA-seq) may provide higher resolution mapping of the early progenitor populations as long as high throughput technology is available to sequence thousands of single cells. Nevertheless, high throughput scRNA-seq is limited in its inability to jointly and robustly detect the mutational status and the transcriptional profile from the same cell. To overcome these limitations, we propose the use of scRNA-seq combined with targeted mutation sequencing from transcrptional read-outs.
Overall design We apply this method to study myeloid neopasms, in which the comlex process of hematopoiesis is corrupted by mutated stem and progenitor cells.
Contributor(s) Kim K, Nam AS, Chaligne R, Smibert P, Landau DA
Citation(s) 31270458
Submission date Jul 27, 2018
Last update date Jul 10, 2019
Contact name Kyu-Tae Kim
Organization name New York Genome Center
Lab Landau Lab
Street address 101 Avenue of the Americas
City New York
State/province New York
ZIP/Postal code 10013
Country USA
Platforms (3)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL22245 Illumina HiSeq 2500 (Homo sapiens; Mus musculus)
Samples (16)
GSM3309838 amplicon.ET01.CALR
GSM3309839 amplicon.ET02.CALR
GSM3309840 amplicon.ET03.CALR
This SubSeries is part of SuperSeries:
GSE117826 Single-Cell Genotyping of Transcriptomes
BioProject PRJNA483242
SRA SRP155570

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
GSE117825_RAW.tar 370.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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