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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 01, 2012 |
Title |
Planarian stem cell transcriptome |
Organism |
Schmidtea mediterranea |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Many long-lived species of animals require the function of adult stem cells throughout their lives. However, the transcriptomes of stem cells in invertebrates and vertebrates have not been compared, and consequently ancestral regulatory circuits that control stem cell populations remain poorly defined. In this study, we have used data from high-throughput RNA sequencing (RNA-Seq) to compare the transcriptomes of pluripotent adult stem cells from planarians with the transcriptomes of human and mouse pluripotent embryonic stem cells. From a stringently-defined set of 4,432 orthologs shared between planarians, mice and humans, we identified 123 conserved genes that are ≥ 5-fold differentially expressed in stem cells from all three species. Guided by this gene set, we used RNAi screening in adult planarians to discover novel stem cell regulators, which we found to affect the stem cell-associated functions of tissue homeostasis, regeneration, and stem cell maintenance. Examples of genes that disrupted these processes included the orthologs of TBL3, PSD12, TTC27, and RACK1. From these analyses, we concluded that by comparing stem cell transcriptomes from diverse species, it is possible to uncover conserved factors that function in stem cell biology. These results provide insights into which genes composed the ancestral circuitry underlying the control of stem cell self-renewal and pluripotency.
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Overall design |
Three planarian tissues were analyzed: stem cells, stem cell progeny, and differentiated tissues. For the manuscript: Labbe, RM, et. al., 2012, Stem Cells
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Contributor(s) |
Pearson BJ |
Citation(s) |
22696458, 26114597 |
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Submission date |
May 10, 2012 |
Last update date |
Jul 30, 2019 |
Contact name |
Bret J Pearson |
E-mail(s) |
pearsobr@ohsu.edu
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Organization name |
Oregon Health and Science University
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Department |
Pediatrics
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Lab |
Pearson
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Street address |
3181 SW Sam Jackson Park Rd., BRB Room 305
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City |
Portland |
State/province |
OR |
ZIP/Postal code |
97239 |
Country |
USA |
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Platforms (2) |
GPL14991 |
Illumina Genome Analyzer IIx (Schmidtea mediterranea) |
GPL15553 |
Illumina HiSeq 2000 (Schmidtea mediterranea) |
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Samples (3) |
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Relations |
SRA |
SRP013005 |
BioProject |
PRJNA167022 |
Supplementary file |
Size |
Download |
File type/resource |
GSE37910_BPKG_transcriptome.nt.txt.gz |
14.0 Mb |
(ftp)(http) |
TXT |
GSE37910_Table_S1.txt.gz |
336.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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