SMED30023469

Overview
NameSMED30023469
Smed IDSMED30023469
Length (bp)1710
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 SMED30023469 (SMED30023469) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023469 (SMED30023469) 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 SMED30023469 (SMED30023469) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023469 (SMED30023469) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30023469

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30023469SMESG000067424.1 dd_Smed_v4_7353_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023469SMESG000067424.1 dd_Smed_v4_7353_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023469SMESG000067424.1 dd_Smed_v4_7353_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30023469SMESG000067424.1 dd_Smed_v4_7353_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023469 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001938:49778..51480 +8497
Homology
[Close]
BLAST of SMED30023469 vs. Planmine SMEST
Match: SMESG000067424.1 (SMESG000067424.1)

HSP 1 Score: 964.14 bits (2491), Expect = 0.000e+0
Identity = 488/490 (99.59%), Postives = 489/490 (99.80%), Query Frame = 3 
Query:  189 MIALFSICKIVTAIYFVFKYASAYSGNISKNSTNKNWCITKTSFNGRKLSCKFQCWKTPNLFLPFENEEWRNSIDSMNLQVIDQNCSNEVDFRNIPTLSSLSNFVLSGHLKTFNLSALLIAAPKLENLLMPLTDLNVLFMEKLSQTNLKSIYLFGKFDPKHWQXXXXXXXXXXXXXXVLNRKIFIPGKLFANMPNIEMINLQIVSDKISSYSFYNLTKLTHLHIHNNNYHTPMKLQKNAFSHLPALESLKITNFDVDYNGTEMDFCEKISENIYHFVLEGSSLLFVERCKEMWKCTKCGIPNSREIQTMEFKSLLTNKSPNNSNLDDILPNPDRIYYLNTSKLVLIDTHITGITSSSLVRFPLLTHYHHHRSWRLHDNSKIFNTLGDIDKFNDNPFEQLLNNQSKLTEVKLSIAVCDCASYDVYRFLIARNVSVFFYCRNLVTNFNLTSIDSWIFHDVYINLMNQKCSGNFLLINLGFVCSCLFFSFRFY 1658
            MIALFSICKIVTAIYFVFKYASAYSGNISKNSTNKNWCITKTSFNGRKLSCKFQCWKTPNLFLPFENEEWRNSI+SMNLQVIDQNCSNEVDFRNIPTLSSLSNFVLSGHLKTFNLSALLIAAPKLENLLMPLTDLNVLFMEKLSQTNLKSIYLFGKFDPKHWQFLKSSEKSLKSFSLVLNRKIFIPGKLFANMPNIEMINLQIVSDKISSYSFYNLTKLTHLHIHNNNYHTPMKLQKNAFSHLPALESLKITNFDVDYNGTEMDFCEKISENIYHFVLEGSSLLFVERC EMWKCTKCGIPNSREIQTMEFKSLLTNKSPNNSNLDDILPNPDRIYYLNTSKLVLIDTHITGITSSSLVRFPLLTHYHHHRSWRLHDNSKIFNTLGDIDKFNDNPFEQLLNNQSKLTEVKLSIAVCDCASYDVYRFLIARNVSVFFYCRNLVTNFNLTSIDSWIFHDVYINLMNQKCSGNFLLINLGFVCSCLFFSFRFY
Sbjct:    1 MIALFSICKIVTAIYFVFKYASAYSGNISKNSTNKNWCITKTSFNGRKLSCKFQCWKTPNLFLPFENEEWRNSINSMNLQVIDQNCSNEVDFRNIPTLSSLSNFVLSGHLKTFNLSALLIAAPKLENLLMPLTDLNVLFMEKLSQTNLKSIYLFGKFDPKHWQFLKSSEKSLKSFSLVLNRKIFIPGKLFANMPNIEMINLQIVSDKISSYSFYNLTKLTHLHIHNNNYHTPMKLQKNAFSHLPALESLKITNFDVDYNGTEMDFCEKISENIYHFVLEGSSLLFVERCNEMWKCTKCGIPNSREIQTMEFKSLLTNKSPNNSNLDDILPNPDRIYYLNTSKLVLIDTHITGITSSSLVRFPLLTHYHHHRSWRLHDNSKIFNTLGDIDKFNDNPFEQLLNNQSKLTEVKLSIAVCDCASYDVYRFLIARNVSVFFYCRNLVTNFNLTSIDSWIFHDVYINLMNQKCSGNFLLINLGFVCSCLFFSFRFY 490
The following BLAST results are available for this feature:
BLAST of SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 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 SMED30023469 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000067424.10.000e+099.59SMESG000067424.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023469 ID=SMED30023469|Name=SMED30023469|organism=Schmidtea mediterranea sexual|type=transcript|length=1710bp
AAAATATGTTAAATTTCTAAATCCGTTTTCATTGGATAATTTAAAATTAC
AAATAATGTTTATTTAAAACGCAATTTCGTGAGAAATAAGTTAAATTACT
TTAACTTGTCTTATTGAACGAACAGGAGAAAATGTAAAACGACGAATTGA
TTTCGATGTGAACAAATTCCGATTTATTTCCATTAGTTATGATAGCACTT
TTTAGTATCTGTAAGATAGTGACAGCGATTTATTTTGTATTCAAATATGC
GAGTGCGTATTCTGGGAATATTTCAAAAAATTCTACTAATAAAAATTGGT
GCATCACTAAAACCTCATTTAACGGCAGGAAACTTTCCTGTAAATTCCAA
TGTTGGAAAACTCCAAATCTCTTTTTGCCATTTGAAAATGAAGAATGGCG
AAATTCAATTGATTCCATGAATTTGCAAGTGATTGATCAAAATTGTAGCA
ATGAAGTCGATTTCAGAAATATTCCAACTTTGAGCAGTTTGTCAAATTTT
GTGTTGAGTGGTCATTTGAAAACATTCAATTTGTCTGCTCTGTTAATTGC
TGCCCCGAAACTCGAAAATTTATTAATGCCTTTGACAGATTTGAATGTTT
TATTCATGGAAAAATTATCGCAAACGAATTTGAAATCAATTTATTTATTT
GGAAAATTCGATCCGAAACATTGGCAGTTTTTAAAGTCATCTGAAAAATC
TCTCAAATCGTTTTCGTTGGTTTTGAACCGAAAGATATTTATTCCCGGGA
AATTATTTGCAAACATGCCAAACATTGAAATGATAAACCTGCAAATCGTG
TCGGACAAAATCAGTTCCTATTCATTTTACAATCTAACCAAGCTTACCCA
TCTCCATATCCACAACAACAACTATCATACTCCAATGAAACTGCAAAAGA
ATGCGTTTAGTCATTTGCCGGCTTTGGAAAGCTTAAAAATTACCAACTTC
GATGTCGACTACAACGGAACGGAAATGGATTTCTGTGAAAAAATCTCCGA
AAACATTTACCATTTTGTTTTGGAAGGATCATCGCTCTTGTTCGTAGAAC
GGTGCAAAGAAATGTGGAAATGTACCAAATGCGGTATTCCAAACAGTAGA
GAAATCCAAACAATGGAATTCAAAAGTCTCCTGACTAACAAATCGCCGAA
TAACTCCAATTTAGACGACATTCTCCCGAATCCCGACAGGATATACTACT
TGAACACCAGTAAATTGGTACTGATTGACACCCACATCACCGGCATCACC
AGCAGCAGTCTGGTGCGGTTTCCTTTGCTTACCCATTACCATCATCATCG
CAGTTGGCGATTGCACGATAATAGCAAAATTTTCAATACGCTTGGTGACA
TCGACAAGTTCAATGATAATCCGTTCGAACAGCTTCTCAACAATCAGTCG
AAATTAACCGAGGTGAAATTATCCATTGCAGTTTGCGATTGCGCCAGTTA
CGATGTTTATCGATTTTTAATCGCCAGAAATGTTTCTGTGTTTTTCTATT
GTCGGAATTTAGTAACAAATTTTAATCTAACTAGCATTGATTCTTGGATA
TTCCACGACGTTTATATCAATTTGATGAATCAGAAATGTTCTGGGAATTT
TCTATTGATTAATTTAGGATTCGTGTGTAGCTGCTTGTTTTTCTCTTTTA
GATTTTATTAACAAACTGTTTATTGTAATTAATAAATTTTGTTTTAATTT
TCAAAAAAAA
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protein sequence of SMED30023469-orf-1

>SMED30023469-orf-1 ID=SMED30023469-orf-1|Name=SMED30023469-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=491bp
MIALFSICKIVTAIYFVFKYASAYSGNISKNSTNKNWCITKTSFNGRKLS
CKFQCWKTPNLFLPFENEEWRNSIDSMNLQVIDQNCSNEVDFRNIPTLSS
LSNFVLSGHLKTFNLSALLIAAPKLENLLMPLTDLNVLFMEKLSQTNLKS
IYLFGKFDPKHWQFLKSSEKSLKSFSLVLNRKIFIPGKLFANMPNIEMIN
LQIVSDKISSYSFYNLTKLTHLHIHNNNYHTPMKLQKNAFSHLPALESLK
ITNFDVDYNGTEMDFCEKISENIYHFVLEGSSLLFVERCKEMWKCTKCGI
PNSREIQTMEFKSLLTNKSPNNSNLDDILPNPDRIYYLNTSKLVLIDTHI
TGITSSSLVRFPLLTHYHHHRSWRLHDNSKIFNTLGDIDKFNDNPFEQLL
NNQSKLTEVKLSIAVCDCASYDVYRFLIARNVSVFFYCRNLVTNFNLTSI
DSWIFHDVYINLMNQKCSGNFLLINLGFVCSCLFFSFRFY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR032675LRR_dom_sf
Vocabulary: molecular function
TermDefinition
GO:0004871signal transducer activity
GO:0004930G-protein coupled receptor activity
GO:0004996thyroid-stimulating hormone receptor activity
GO:0008528G-protein coupled peptide receptor activity
GO:0016500protein-hormone receptor activity
Vocabulary: cellular component
TermDefinition
GO:0005886plasma membrane
GO:0005887integral component of plasma membrane
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: biological process
TermDefinition
GO:0007165signal transduction
GO:0007186G-protein coupled receptor signaling pathway
GO:0007189adenylate cyclase-activating G-protein coupled receptor signaling pathway
GO:0007190activation of adenylate cyclase activity
GO:0007399nervous system development
GO:0009755hormone-mediated signaling pathway
GO:0038194thyroid-stimulating hormone signaling pathway
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR032675Leucine-rich repeat domain superfamilyGENE3DG3DSA:3.80.10.10coord: 133..272
e-value: 2.2E-10
score: 42.6
NoneNo IPR availableSUPERFAMILYSSF52058L domain-likecoord: 171..253