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Series GSE106269 Query DataSets for GSE106269
Status Public on Sep 27, 2018
Title Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration
Organism Ambystoma mexicanum
Experiment type Expression profiling by high throughput sequencing
Summary Amputation of the axolotl forelimb results in the formation of a blastema, a transient tissue where progenitor cells accumulate prior to limb regeneration. Connective tissue (CT) – skeleton, periskeleton, tendon, dermis, interstitial cells – contributes the vast majority of cells that populate the blastema, however it is unclear how individual CT cells may reprogram their fate in order to rebuild the tetrapod limb. Here we use a combination of Cre-loxP reporter lineage tracking and single-cell (sc) RNA-seq to molecularly track, for the first time, adult CT cell heterogeneity and its transition to a limb blastema state. We uncover a multi-phasic molecular program where CT cell types found in the uninjured adult limb revert to a relatively homogenous progenitor state that participates in inflammation and extracellular matrix disassembly prior to proliferation, establishment of positional information, and ultimately re-differentiation. While the early regeneration transcriptome states are unique to the blastema, the later stages recapitulate embryonic limb development. Notably, we do not find evidence of a pre-existing blastema-like precursor nor limb bud-like progenitors in the uninjured adult tissue. However, we find that distinct CT subpopulations in the adult limb differentially contribute to proximal and distal portions of the regenerated limb. Together, our data illuminates molecular and cellular reprogramming during complex organ regeneration in a vertebrate.
 
Overall design Single-cell transcriptomics and reporter lineage tracking was used to deconstruct cell composition, reconstruct lineage relationships, and trace connective tissue reprogramming during axolotl limb regeneration.
 
Contributor(s) Gerber T, Treutlein B
Citation(s) 30262634
Submission date Oct 27, 2017
Last update date Oct 22, 2018
Contact name Tobias Gerber
E-mail(s) tobias.gerber@embl.de
Organization name EMBL Heidelberg
Department Developmental Biology
Lab Detlev Arendt
Street address Meyerhofstr. 1
City Heidelberg
ZIP/Postal code 69117
Country Germany
 
Platforms (1)
GPL22800 Illumina HiSeq 2500 (Ambystoma mexicanum)
Samples (1604)
GSM3204856 axo2.A1
GSM3204857 axo2.A10
GSM3204858 axo2.A12
Relations
BioProject PRJNA416091
SRA SRP122505

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
GSE106269_RAW.tar 172.4 Mb (http)(custom) TAR (of MTX, TSV)
GSE106269_Table_S3.csv.gz 5.0 Mb (ftp)(http) CSV
GSE106269_Table_S5.csv.gz 4.7 Mb (ftp)(http) CSV
GSE106269_Table_S7.csv.gz 31.3 Mb (ftp)(http) CSV
GSE106269_Table_S8.csv.gz 11.9 Mb (ftp)(http) CSV
GSE106269_Table_S9.csv.gz 45.7 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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