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Series GSE111764 Query DataSets for GSE111764
Status Public on Apr 17, 2018
Title Cell type transcriptome atlas for the planarian Schmidtea mediterranea
Organisms Homo sapiens; Mus musculus; Schmidtea mediterranea
Experiment type Expression profiling by high throughput sequencing
Summary The transcriptome of a cell dictates its unique cell-type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Schmidtea mediterranea. Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells. We also uncovered regionally expressed genes in muscle, which harbors positional information. Identifying the transcriptomes for potentially all cell types for many organisms should be readily attainable and is a powerful new approach to metazoan biology.
Overall design Single cell transcriptomes for the planarian Schmidtea mediterranea were generated using Drop-seq.
Please note that each processed data file was generated from multiple samples, as indicated in the corresposponding sample description field.
Contributor(s) Fincher CT, Wurtzel O, de Hoog T, Kravarik KM, Reddien PW
Citation(s) 29674431, 30962434
Submission date Mar 13, 2018
Last update date Apr 17, 2019
Contact name Christopher Fincher
Organization name Whitehead Institute
Lab Reddien
Street address 455 Main St
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (2)
GPL19969 Illumina MiSeq (Homo sapiens; Mus musculus)
GPL21689 Illumina NextSeq 500 (Schmidtea mediterranea)
Samples (32)
GSM3039452 Whole animal 1.1
GSM3039453 Head 1
GSM3039454 Head 2
BioProject PRJNA438083
SRA SRP135258

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE111764_BrainClusteringDigitalExpressionMatrix.dge.txt.gz 14.5 Mb (ftp)(http) TXT
GSE111764_PrincipalClusteringDigitalExpressionMatrix.dge.txt.gz 91.8 Mb (ftp)(http) TXT
GSE111764_Saturation.txt.gz 2.1 Mb (ftp)(http) TXT
GSE111764_SexualClusteringDigitalExpressionMatrix.dge.txt.gz 19.8 Mb (ftp)(http) TXT
GSE111764_SpeciesMixing_Human.dge.txt.gz 430.8 Kb (ftp)(http) TXT
GSE111764_SpeciesMixing_Mouse.dge.txt.gz 387.0 Kb (ftp)(http) TXT
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Processed data are available on Series record

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