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Series GSE159544 Query DataSets for GSE159544
Status Public on Mar 13, 2023
Title Hypertrophic chondrocytes and osteogenesis in P6 mouse tibia
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary It has been shown that hypertrophic chondrocyte (HC) can become osteoblast, contributing to the formation of trabecular bone and endosteum. However, it is unclear what genes regulate the process of differentiation from chondrocyte to osteoblast. Conditional knock-out of Irx 3 and Irx5 in HCs can reduce the trabecular bone amount and there is also some evidence that ablation of Irx3 and Irx5 in HCs can promote bone marrow adipogenesis. In order to investigate the gene regulatory network with different dosage of Irx3/5 in HC descendants (i.e. in Loss-of-Function mutant and heterozygous control), we collected HC descendant cells from proximal tibia of mice at postnatal day 6 and performed single cell RNA seq with 10X Genomics System to profile the gene expression pattern in HC descendants.
 
Overall design We sequenced one sample. Cells were harvested from proximal and distal tibia. The sample (a pool of two tibia from the same male P6 mouse) is on Col10a1Cre;Rosa26-Tdtomato;Irx3 +/Δ;Irx5 +/- (Irx3/5 heterozygous control). Cells with or without Tdtomato fluoresence are digested out by sequential digestion, enriched by sequential centrifugation and resuspension and subject to standard 10X Genomics protocol.
 
Contributor(s) Zhijia T, Mingpeng K, Chen P, Cheah KS
Citation(s) 36892459
Submission date Oct 19, 2020
Last update date Mar 13, 2023
Contact name Peikai Chen
E-mail(s) pkchen1@hku.hk
Phone 852-258315217
Organization name The University of Hong Kong
Department Faculty of Medicine
Street address Sassoon Road 5
City Pok Fu Lam
ZIP/Postal code 10000
Country Hong Kong
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM4832257 Irx3/5-het-P6 [S17]
GSM4832258 Irx3/5-het-P6 [S18]
GSM4832259 Irx3/5-het-P6 [S19]
Relations
BioProject PRJNA670007
SRA SRP287836

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
GSE159544_barcodes.tsv.gz 68.8 Kb (ftp)(http) TSV
GSE159544_exo_barcodes.tsv.gz 20.0 Mb (ftp)(http) TSV
GSE159544_exo_features.tsv.gz 592 b (ftp)(http) TSV
GSE159544_exo_matrix.mtx.gz 27.3 Kb (ftp)(http) MTX
GSE159544_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE159544_matrix.mtx.gz 120.7 Mb (ftp)(http) MTX
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Raw data are available in SRA
Processed data are available on Series record

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