SMED30003904

Overview
NameSMED30003904
Smed IDSMED30003904
Length (bp)759
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30003904 (SMED30003904) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003904 (SMED30003904) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30003904

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30003904SMESG000024141.1 Contig3334newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
zeta neoblastSMED30003904 dd_Smed_v4_18353_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30003904 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001078:75013..75770 +3395
Homology
BLAST of SMED30003904 vs. TrEMBL
Match: A0A0L8HS33 (DDE_Tnp_IS1595 domain-containing protein (Fragment) OS=Octopus bimaculoides OX=37653 GN=OCBIM_22007566mg PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 4.551e-13
Identity = 35/71 (49.30%), Postives = 49/71 (69.01%), Query Frame = -1
Query:  115 VHQQNFGDPTDNQVHTKIVENM*M--QPKLKRQFGTSRALFPSYLHEFTYRNQFRQQDVFLNFIIAIAEYY 321
            VH+ +F DP DN +HT+ +EN+ M  + KL  QFGTS  LF SYLHEF +RN   ++ +F+ F+ AI+E Y
Sbjct:   28 VHEDHFVDPNDNGIHTQNIENLWMRLKRKLWWQFGTSDELFSSYLHEFLWRNSTPKEKIFVYFLAAISEVY 98          
BLAST of SMED30003904 vs. TrEMBL
Match: D6WRA6 (Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC010016 PE=4 SV=2)

HSP 1 Score: 74.3294 bits (181), Expect = 4.413e-12
Identity = 38/73 (52.05%), Postives = 53/73 (72.60%), Query Frame = -1
Query:  115 VHQQNFGDPTDNQVHTKIVENM*MQPK--LKRQFGTSRALFPSYLHEFTYRNQFRQ-QDVFLN-FIIAIAEYY 321
            +H+QNF +P D ++HT+ VEN+ M+ K  L+RQFGTS  LF SYLHEF +RN+FRQ +D   N F++ I + Y
Sbjct:  166 IHEQNFVNPNDPEIHTQNVENLWMRTKHKLRRQFGTSEDLFVSYLHEFIWRNKFRQVRDYLFNEFLLCIVKQY 238          
BLAST of SMED30003904 vs. TrEMBL
Match: A0A0L8FW94 (DDE_Tnp_IS1595 domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22006020mg PE=4 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 5.001e-11
Identity = 34/71 (47.89%), Postives = 49/71 (69.01%), Query Frame = -1
Query:  115 VHQQNFGDPTDNQVHTKIVENM*M--QPKLKRQFGTSRALFPSYLHEFTYRNQFRQQDVFLNFIIAIAEYY 321
            VH  +F DP DN++HT+ +EN+ M  + KL+ Q+GTS  LF SYLHEF +RN   ++  F+ F+ AI+E Y
Sbjct:  237 VHGDHFVDPNDNEIHTQNIENLWMRLKRKLRWQYGTSDELFLSYLHEFLWRNSIPKEKTFVYFLAAISEVY 307          
BLAST of SMED30003904 vs. TrEMBL
Match: A0A0L8FI20 (Uncharacterized protein (Fragment) OS=Octopus bimaculoides OX=37653 GN=OCBIM_22020397mg PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 4.397e-7
Identity = 28/48 (58.33%), Postives = 36/48 (75.00%), Query Frame = -1
Query:  184 VHQQNFGDPTDNQVHTKIVENM*MQPK--LKRQFGTSRALFPSYLHEF 321
            +HQQNF DP +  VHT+ VE++ ++ K  L+RQFGTS  LF SYLHEF
Sbjct:    8 IHQQNFVDPHNQHVHTQNVESIWVRVKRVLRRQFGTSDELFVSYLHEF 55          
BLAST of SMED30003904 vs. TrEMBL
Match: W4Z0I9 (DDE_Tnp_IS1595 domain-containing protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 9.168e-7
Identity = 28/52 (53.85%), Postives = 35/52 (67.31%), Query Frame = -1
Query:  172 VHQQNFGDPTDNQVHTKIVENM*--MQPKLKRQFGTSRALFPSYLHEFTYRN 321
            +H+ NF DP    +HT  +E      + KL+RQFGTSRALFPSYL EF +RN
Sbjct:  253 IHEDNFVDPVHEWLHTNTIEGKWNHAKRKLRRQFGTSRALFPSYLDEFMWRN 304          
The following BLAST results are available for this feature:
BLAST of SMED30003904 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 SMED30003904 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 SMED30003904 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 SMED30003904 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 SMED30003904 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 SMED30003904 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 SMED30003904 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 SMED30003904 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0L8HS334.551e-1349.30DDE_Tnp_IS1595 domain-containing protein (Fragment... [more]
D6WRA64.413e-1252.05Uncharacterized protein OS=Tribolium castaneum OX=... [more]
A0A0L8FW945.001e-1147.89DDE_Tnp_IS1595 domain-containing protein OS=Octopu... [more]
A0A0L8FI204.397e-758.33Uncharacterized protein (Fragment) OS=Octopus bima... [more]
W4Z0I99.168e-753.85DDE_Tnp_IS1595 domain-containing protein OS=Strong... [more]
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BLAST of SMED30003904 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 SMED30003904 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 SMED30003904 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 SMED30003904 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 SMED30003904 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 SMED30003904 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

>SMED30003904 ID=SMED30003904|Name=SMED30003904|organism=Schmidtea mediterranea sexual|type=transcript|length=759bp
ATTGTATATTTAGAATTATATAGAATAAGAAATGACTGACAAATTTTATT
TATGAAGCAAAACTGTTATTAAGCGTACAGTGAGGATAGTGTCATGAAAT
AAATGTTACTTAACATAATACTCAGCGATTGCAATAATGAAGTTAAGAAA
TACATCTTGTTGACGAAACTGATTCCTGTACGTAAATTCATGTAGGTATG
AAGGAAACAAAGCACGGCTGGTTCCAAACTGACGTTTCAGTTTGGGTTGC
ATTCACATATTTTCTACAATCTTGGTGTGAACTTGGTTATCTGTCGGATC
ACCAAAGTTCTGTTGGTGGACATACGAACCTCGTCCCGTGAATCCCTTGC
TGTATGTTTGAAGTGTGCACAGCTGACTACATACATTAGATTTTATTGTG
TTGCGAATCAAACTTCTAGATGCGCACCACTTGAATGCCGAGAAGGGGTA
TTTCATTTATGCAGCTAATGACGACAATCGCCATACCTGCTGTTTAGAAC
AAGATTAACAGTAACAATGCTAGTGGCATTCCTTGGTCTCCCAGCCATGA
TTATTCAAATAACCGATTTATAAATATTTTTTAATAAATATATCGATTTA
ATATGGCTGACATACTGACGAAGAGTAAGTAAAAAAATTAAATTCCAGGC
GCTAAAACCCAAGTTTATATGGATGTATAAAAACATTTCAATGATTAAAA
TAAATTTTTCATTATATTTGGCAAAATCTAAGTGTTATTTGATAATATGA
ATTGGTAAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000070intestinal phagocyte