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Series GSE182202 Query DataSets for GSE182202
Status Public on Aug 01, 2022
Title Single cell transcriptomic analysis of P8 and P15 mouse cochlea (control and three overexpression conditions) and simultaneous single cell transcriptomic and accessible chromatin analysis of P1 and P8 mouse cochlea (wildtype)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose - To determine transcriptomic variations in the mouse cochlea in response to three different transcription factor overexpression conditions and no induction control and to determine transcriptomic and accessible chromatin variations in the mouse cochlea between postnatal day 1 (P1) and postnatal day 8 (P8) stages of development.
Methods - SC RNA seq performed on FACS enriched cells obtained from experimental animals (Sox9CreER; Rosa26A/GA/GAP/+; Rosa26 tdtomato). Same samples at two timepoints 1 week (P8) and 2 week (P15) ages. scMultiome ATAC + Gene Expression (10x Genomics) experiments on enzymatically dissociated and unenriched cochlear nuclei from wildtype mice in a mixed background of CD1 and FVB/NJ, and C57BL/6. Samples were collected at P1 and P8. Gene expression data was used to annotate clusters. Chromatin accessibility determined by ATAC was compared between P1 and P8 stages.
Results - The SC RNA seq highlighted differential transcriptomic changes between the two ages and the three overexpression conditions. Hair cell loci become less epigenetically accessible in supporting cells and GER cells between P1 and P8.
Conclusions - Our study highlights the variability in transcriptomic response to three transcription factor combination mediated reprogramming cues at two different ages. The SC RNA seq confirmed a variety of our biological observations with regard to the hair cell reprogramming process in the mouse cochlea. We also demonstrate variability in chromatin accessibility between P1 and P8, which may explain why GER and supporting cells of the cochlea become more resistant to transcription factor reprogramming into hair cells during the first postnatal week.
Overall design Examination of transcriptome via single cell RNA seq of FACS purified mouse cochlear cells at P8 and P15 induced with transcription factor combinations. scMultiome ATAC + Gene Expression (10x Genomics) experiments on P1 and P8 wildtype cochlea sensory epithelium.
Contributor(s) Groves AK, Segil N, Iyer AA, Hosamani I, Nguyen JD
Citation(s) 36445327
Submission date Aug 16, 2021
Last update date Dec 24, 2022
Contact name Andrew K Groves
Organization name Baylor College of Medicine
Street address One Baylor Plaza, Baylor College of Medicine
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (12)
GSM5520356 S9WT-P8
GSM5520357 S9Rosa26A-P8
GSM5520358 S9Rosa26GA-P8
BioProject PRJNA755297
SRA SRP332719

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
GSE182202_P1_cochlea_wildtype_10x_scRNA_scATAC_cluster_annotation.tsv.gz 25.6 Kb (ftp)(http) TSV
GSE182202_P8_cochlea_wildtype_10x_scRNA_scATAC_cluster_annotation.tsv.gz 35.7 Kb (ftp)(http) TSV
GSE182202_RAW.tar 8.6 Gb (http)(custom) TAR (of MTX, TAR, TSV)
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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