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Series GSE151985 Query DataSets for GSE151985
Status Public on Jun 23, 2020
Title A single cell transcriptional atlas of early synovial joint development
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Synovial joint development begins with the formation of the interzone, a region of condensed mesenchymal cells at the site of the prospective joint. Recently, lineage tracing strategies have revealed that Gdf5-lineage cells native to and from outside the interzone contribute to most, if not all, of the major joint components. However, there is limited knowledge of the specific transcriptional and signaling programs that regulate interzone formation and fate diversification of synovial joint constituents. To address this, we have performed single cell RNA-Seq analysis of 7,329 synovial joint progenitor cells from the developing murine knee joint from E12.5 to E15.5. By using a combination of computational analytics, in situ hybridization, and in vitro characterization of prospectively isolated populations, we have identified the transcriptional profiles of the major developmental paths for joint progenitors. Our freely available single cell transcriptional atlas will serve as a resource for the community to uncover transcriptional programs and cell interactions that regulate synovial joint development.
Overall design We sampled Gdf5-lineage cells of the murine knee at embryonic time points e12.5, e13.5, e14.5, and e15.5 and subjected them to single cell RNAseq analysis via 10x.
Contributor(s) Bian Q, Cahan P
Citation(s) 32580935
NIH grant(s)
Grant ID Grant title Affiliation Name
R35 GM124725 From intra to intercellular regulatory networks that define cell type identity JOHNS HOPKINS UNIVERSITY Patrick Cahan
Submission date Jun 08, 2020
Last update date Sep 22, 2020
Contact name Patrick Cahan
Organization name Johns Hopkins University School of Medicine
Department ICE and Biomedical Engineering
Lab Cahan Lab
Street address 733 North Broadway, MRB 653
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (4)
GSM4594552 e12_5
GSM4594553 e13_5
GSM4594554 e14_5
BioProject PRJNA638016
SRA SRP266397

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE151985_RAW.tar 103.7 Mb (http)(custom) TAR (of TAR)
GSE151985_annData_GLE_cells.h5ad.gz 111.8 Mb (ftp)(http) H5AD
GSE151985_annData_nonjoint_cells.h5ad.gz 39.6 Mb (ftp)(http) H5AD
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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