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Series GSE114157 Query DataSets for GSE114157
Status Public on Mar 12, 2019
Title Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The goal of this study was to isolate individual cochlear hair cells and supporting cells from wild type animals in order to characterize the transcriptome of functionally mature auditory hair cells in the mammalian cochlea.
Overall design Single-cell RNA sequencing is a powerful tool by which to characterize the transcriptional profile of low-abundance cell types, however its application to the inner ear has been hampered by the bony labyrinth, tissue sparsity and difficulties in dissociating the ultra-rare cells of the membranous cochlea.  Herein, we present a method to isolate individual inner hair cells (IHCs), outer hair cells (OHCs) and Deiters’ cells (DCs) from the murine cochlea at any post-natal time point. We isolated of 132 single cells from OHC, IHC, and DC cell types at postnatal day 15 (p15) and performed RNA-Sequencing of these cells using smartseq2 and Illumina HiSeq. An additional 12 single OHCs from the same timepoint were isolated and sequenced using smartseq2 and the Nanopore MinION 1D reads. We leverage single-cell RNA sequencing to analyze these three cell types and generate a multidimensional overview of their transcriptomes. The data provide new insights into OHC motility and the architecture of gene products implicated in hereditary hearing loss. This refined view of transcription in the organ of Corti will enhance to our understanding of the biology of hearing and deafness.
Contributor(s) Ranum PT, Smith RJ
Citation(s) 30865901
Submission date May 08, 2018
Last update date Mar 28, 2019
Contact name Paul T Ranum
Phone 1 (651) 398-6455
Organization name The Children's Hospital of Philadelphia
Department Center for Cellular and Molecular Therapy
Lab Davidson Lab
Street address 3501 Civic Center Blvd.
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24973 MinION (Mus musculus)
Samples (144)
GSM3135715 IHC_128
GSM3135716 OHC_129
GSM3135717 OHC_130
BioProject PRJNA464433
SRA SRP147921

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
GSE114157_Nano_Gene_Expression.txt.gz 965.8 Kb (ftp)(http) TXT
GSE114157_Nano_Isoform_expression.txt.gz 311.5 Kb (ftp)(http) TXT
GSE114157_Nano_Isoforms.txt.gz 488.7 Kb (ftp)(http) TXT
GSE114157_Nano_TESS.bed.gz 3.3 Mb (ftp)(http) BED
GSE114157_Nano_ss.bed.gz 7.1 Mb (ftp)(http) BED
GSE114157_RAW.tar 1.8 Gb (http)(custom) TAR (of FASTA, PSL, TSV)
GSE114157_p15_Expression_Matrix.csv.gz 2.1 Mb (ftp)(http) CSV
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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