SMED30020402

Overview
NameSMED30020402
Smed IDSMED30020402
Length (bp)4897
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30020402 (SMED30020402) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020402 (SMED30020402) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30020402 (SMED30020402) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020402 (SMED30020402) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30020402

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30020402SMESG000011919.1 dd_Smed_v4_1147_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020402SMESG000011919.1 dd_Smed_v4_1147_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020402SMESG000011919.1 dd_Smed_v4_1147_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020402SMESG000011919.1 dd_Smed_v4_1147_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020402SMESG000011919.1 dd_Smed_v4_1147_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30020402SMESG000011919.1 dd_Smed_v4_1147_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020402 Contig52788newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
neuronSMED30020402SMESG000011919.1 dd_Smed_v6_1147_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cholinergic neuronSMED30020402SMESG000011919.1 dd_Smed_v6_1147_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pigment cellSMED30020402SMESG000011919.1 dd_Smed_v6_1147_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020402 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002340:34571..39462 +23817
Homology
The following BLAST results are available for this feature:
BLAST of SMED30020402 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020402 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020402 ID=SMED30020402|Name=SMED30020402|organism=Schmidtea mediterranea sexual|type=transcript|length=4897bp
AATGGCAAATTAAATAAACAAATATTAATATTGATAATAAACGAATGATA
TTAATTAATATATTGATCTAAATAATTATATATCTATATTGATGGATATC
AATTGTTGAATATTATGTAAATATGCTCTCATTCACTCTTATTCAAAAGG
ATGTATAAATTAAATATCATTCGTTTTATGGGGTTTATCAACGGTTCCCC
TGAATCTCGCGTTTAGAGTACTCAAAATAATTATAATAAACTCAGATTTT
GTCTACAAATAGTCGTACATATTCTGTGGTTGATATTTTCTGTCAATTTT
ACAGTCCGATTATGTGATGATTTATCAAATCTCAGTGGGCTTTGCTTTCA
AGTATTTGAGTTGCACCTAAATGTTGCAACCAATTGGTGCTTATAGGACA
ATTTTCAGAACCAATTCGATTTTGTTAATTAATTTGTAGTTCTCAAGCAC
TCAGTTACTGTAAATCACTTCAGCTTAGGCTTTTTATCGATGCAATTATT
AATTACGTCACATGAAACTAAAAATATTGATTATTATCAAAAATATTTTA
ATTGGAATTTAATCAACTTTTCCATATAAATTAGCTATTACTTGTAGCTT
CGATAGGATTATATCATATAATATTACATTTTACGGTTAAATAATACATT
TTGGTCAATTAATTTCTACTGTTGATTTATTGATTTTTTTATTTTATGAA
TAATCATTTAGTATCATGGTTTTATCAAATTTGTATAGATTTTCTGTTTT
TAATGTTCATTTTTGACATGAATACCAAAAATTATATTGATTTTAATCTG
TATAACTTGAACTTTTCTGGAACAAGTGAAAAGAAACCCGTGTATATGAA
TAAAACGTGTATTCCAAATCTTTAAATAAATCAAATAATAAGAAACAAAT
TAATAAATAAATTCTATTCAAGTTTTTATTTTATCTTATTAAATTGATTT
TTATCGTCAAAAATTTAAATATGCCATAATTGGAATTATTTATTGATTTG
GAACTTTCGATTGAACTCAAATATTAACATTACACTGAATACAATCATAT
TTTATCTTAACACGTTGAAGACCGCATTGCAAAATCGTATTTCTCACAGA
TAGACCGGCATATTTTTTAGTGTACAATAATTTGAGGTAGACATTATTTA
ACCACTAGATTTATTTCGACTACTGTACATAAATTGAATTTAAATATTTC
ACACCAAAGAACAAATGGTCCCCAAGTAAAACATGTCGTGTGCCCACTCG
TGAGGACGCTGGCCGGTAATGTTGTTTTGGAGTGACCCGTCGGGGAACAT
ACGGTCTTTAACGTGTTAAAGAAGCCATTAAATTTACTCGTTCTATTGTC
GATTTTTACTGCTCGCATCGTACTGATAAACAGTTTCATTCTCATGCATT
AACTCCACATATATATACCTCGAGATTTAGGGTACAGTACACTTTTGCAA
CTATAAATTTGACAGTAAATGACGCATGCTATTGCTGATTTTAACGTAAT
ATTGGTCTCTGTAATTTTCCGATTATTTATCAAAAAATCAATGTTTATTT
GAAAATAAATTTTTCTTGATCGTTATTTTTTTACTGGTCTCGTAATACTT
AAAAGAAAGCTAGCGCATTTACCCTAATCAAATACTCAGAAACAACCATC
TTTAGTTTTTTATAATTTAGTTCGATTTTGCATATCATAATCAATATTTG
TTTATAAAATAGAAAAGTCGTGTAGTGTAAGATTAACATTCCAAATTATA
GAATCTGTAACTGGAATATAATCGAACTTGTTATAACGCGATTCAAAAAT
TACGACTATTATTACATAACATATAACTCATATAGTATCAGTTTTTTTTA
TCACATACAATTGAAATAAACGTAATTTCTATGCTTACTTAATTCTCCTA
CATTATGGTTTCTTATCAAAACAAATTCAGACATAATAAATAACTGTTTG
ATATTCATTATCTTAATTTTACCTGTGTGTTCAAGAGATTTCATTTTTAA
AATTAAATAAGTAATTTTTCATTTAAAACAAATCAACATTTTCTAATGCC
AGTTCTTGATTTTTAAACATCCAAGTTAAAATTTATACTAATTTGTCTAT
TTTCCCGCGAAGATTGTTCAAACTGAATAAAAACATCCAAAAGTCCTAGG
AGTTGTTTTAAAATTCACACAATCAGATAATTTGACACGATTTTCATAAA
GATTGTTGTGAAATTTTTAAATAAGAATAAAGATTTCCCCAGGTGCAATA
ATGAATATCGTTTATCGGTAAACAAATTATCATTTTCAAAACATATTAAC
GAGCTTCTGATTTCCTTTTAACAATCTTTGTTTTAACGTGGAAAACCAAA
TTCACAATATTCAGTCAGGACTTTTATTCATTTTCATTGCATTTAACAAT
ATTTGATATACGAGGAATGTATTCCTTTGTTTACACAAACAAATCCCATT
CACAGTAATTGCACCTCCATTTCTGTACAACCTATCGTATCCTTTTTAAT
TTAAATCATGATCTTTCTCTGATAAGATTATAAATAATAAAAATACACAC
GAAATAAAAATAATTAGGGTGTTATTTTTAATGTAAACGAAAACATTTAT
TTTTGATTTCTGTCAATATTTGAAATTTTTTGTTTTTTGGTAAGTGTGGC
TTGATTTTGTATAATATTAATGATATTCTATTCAGAAATTGTAAATTATC
AATTTGTTTTATTTGATTACGAATTTACAAACGCAAATCATCAATTTTAC
ACGAATATTGATCGTGGAAATACCGGGCAATTTTTAAACGAGGAGCATGT
ATTGTTCTATATAGTCGTTACGTAGAATAATAATTAGTACACCTTTCTTG
AATACACCAAAATTACTGATAGGAAGCAACCGTTTAATAAACTAACTGAC
GAAAGGAACGGTAAATATGAAGTAGTAGAATTAAAATTTTTACAGCAAGT
TTCAAATTATATATGCAAGATACTTTTTCAAAACGTGATTTGATTTATGT
TTACATTTCGGAACCCAATGGTGCCATTCTGTAGAGTTGTTGAAATTTCC
AAATACTTCCTTGTACTTAAACACAAAATAAGCGAAACATTAAGAAATGA
ATCAATATTAATTTGTTATTAATATTTATCAGTTTTTCTAATTTCAAAAT
AATTTAAGTTGTATGAGAATTCTTATTATGTAATTAAAATTTAATCATTG
ATTTTGGTACAGATATAATTTCGGTAGAGAATAATACATATATCCTATAT
TTAATCGCTGTTCCATGTTTAATTTCTCCTATTGGCTACACAATCTTCGG
TTGACACTTCATTCGAGTGTGGTACTGGGAAATTGGGGTTAGACATTTAA
CATGACATCGTATTGCACTATTGTGATGAATTTATTATTAATATTTTATA
TGTTAATTTTCTCTTTAATTATAATCCAGTCTAAAAATGACAATAAAATA
TAATCACATTCAAAATCGATTTAAAATACTAGTAGTTCATAAAATGAAAT
AACAACATAATTTGATATATCAAAAGGAACAATCAATACAAAAAAAGAAA
TTAATAATCCAATGGAATATTTTTTATAAATCAGTTTTTATGTAATTTAA
AAAAGAAAACAAATCGAACATTTTTATCTTTGTAAATCATTTCATAATCC
AACATTTTTAGTTTTTTTAGAAATTTCGATCAAAGAAACAATTTGTGGAT
ATCTGAGTAAATGTGTTGACAGTGGTCTAAATCTCTTGATTATACACTTA
CAATATACGGATATCTAAATATAGGTGGTCCGTTTTAATTTATTTTCAAG
TAAATTATTGAGCATCAAATTATTGAAACGATTTTTAATATTTCGTAATT
CTTTTATTTTAAATCATATAATGAAAATATATGCGAGTGTGTGTATTTTA
ATAATGAATTTCTACTAGAATAGACCTAAGATAAACCAAACCATATTTTA
CTATTATTATCATTATTATTATTGTTTATTCTTATGTATATTGTCTACAT
TATCATCCAGTATTTAATTAATAGAATTGCAATCTTTTTTATGTGTAAAT
TTGATCATAATTCATTTGTAAAAGCAATATTCAGGATATGTCATAAACAC
GTCATCTTTAATGAATCATCACAAAGAGTTTTTATCTAAAATAAATTTAC
CAGTAAAACCCAAAGTACGTGTCTCTATTCTGGCCATGAAAAAAGTAAAT
GCTCTAATTCAAATTCCGAGTGACTAGCCTATCGATATCAGTGAAGAAGA
TAGTCTTACTCTGGCCAATATAAGGAAAGTAAATTTAAATTGGTAAGAAT
ACTGTATTGTCGTCAGGCATCTTGGACATCATTTAGAATCAAACATATTT
TTTTTTAATAAGTCACTAGGATAGATAATATAAAATACATTAGCTTTTGA
TATAAATAATAATAATGCTATAATAGTTATTGATTTCGTATGATGAGTGG
TTTGTTGGTCAAAGAATGAGATTTATTGAATGAATTTGAAATTTATATTT
TATAATATATGCAGGGAGAAAAAATAGGTATCAAAATGTATTTTGTAAAT
TAAATGAGCGCAGTAGAAATGTTGATTTTATCCTATGTGAAATTAATGAA
AGATCTACTGAAATAATATATACGAAAGTGGATTATATTTTTTGAGCAAC
AGGAATAATTATTGTTTCGAACTCTTTATTTGGAATATAAATATATTAGT
TTTGATACGCTATTTGAATGGAATAGCCAAATATTTTTTTCGTATTTTCG
CCAGCTATTTAACACTTTGAATATAATGACCTTAAAAAGGGTCATATTTT
CAGCTACTATTTGGAAATTTACTTTCATAGAAAATAGTTGATAATAATGT
GTCATGATATTAAAAATAGATTTTTTCGAAAGAAATTTTGGATCAGT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000463cholinergic neuron
PLANA:0002075pigment cell