SMED30028437

Overview
NameSMED30028437
Smed IDSMED30028437
Length (bp)511
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 SMED30028437 (SMED30028437) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028437 (SMED30028437) 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 SMED30028437 (SMED30028437) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028437 (SMED30028437) 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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Homology
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BLAST of SMED30028437 vs. Ensembl Human
Match: SETMAR (SET domain and mariner transposase fusion gene [Source:HGNC Symbol;Acc:HGNC:10762])

HSP 1 Score: 52.373 bits (124), Expect = 3.170e-8
Identity = 25/57 (43.86%), Postives = 35/57 (61.40%), Query Frame = 2 
Query:  341 LKNHDLRLFYLYEWKSKNNSVEAERNINNAFGSDTANEGTIRLWF*KIDEGEIYLEN 511
            L    +R  +L+E+K    + E  RNINNAFG  TANE T++ WF K  +G+  LE+
Sbjct:  110 LDKKQIRAIFLFEFKMGRKAAETTRNINNAFGPGTANERTVQWWFKKFCKGDESLED 166
[Close]
BLAST of SMED30028437 vs. Ensembl Human
Match: SETMAR (SET domain and mariner transposase fusion gene [Source:HGNC Symbol;Acc:HGNC:10762])

HSP 1 Score: 53.1434 bits (126), Expect = 4.199e-8
Identity = 25/57 (43.86%), Postives = 35/57 (61.40%), Query Frame = 2 
Query:  341 LKNHDLRLFYLYEWKSKNNSVEAERNINNAFGSDTANEGTIRLWF*KIDEGEIYLEN 511
            L    +R  +L+E+K    + E  RNINNAFG  TANE T++ WF K  +G+  LE+
Sbjct:  346 LDKKQIRAIFLFEFKMGRKAAETTRNINNAFGPGTANERTVQWWFKKFCKGDESLED 402
[Close]
BLAST of SMED30028437 vs. Ensembl Human
Match: SETMAR (SET domain and mariner transposase fusion gene [Source:HGNC Symbol;Acc:HGNC:10762])

HSP 1 Score: 52.7582 bits (125), Expect = 4.859e-8
Identity = 25/57 (43.86%), Postives = 35/57 (61.40%), Query Frame = 2 
Query:  341 LKNHDLRLFYLYEWKSKNNSVEAERNINNAFGSDTANEGTIRLWF*KIDEGEIYLEN 511
            L    +R  +L+E+K    + E  RNINNAFG  TANE T++ WF K  +G+  LE+
Sbjct:  207 LDKKQIRAIFLFEFKMGRKAAETTRNINNAFGPGTANERTVQWWFKKFCKGDESLED 263
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BLAST of SMED30028437 vs. UniProt/SwissProt
Match: sp|Q53H47|SETMR_HUMAN (Histone-lysine N-methyltransferase SETMAR OS=Homo sapiens OX=9606 GN=SETMAR PE=1 SV=2)

HSP 1 Score: 53.1434 bits (126), Expect = 2.017e-7
Identity = 25/57 (43.86%), Postives = 35/57 (61.40%), Query Frame = 2 
Query:  341 LKNHDLRLFYLYEWKSKNNSVEAERNINNAFGSDTANEGTIRLWF*KIDEGEIYLEN 511
            L    +R  +L+E+K    + E  RNINNAFG  TANE T++ WF K  +G+  LE+
Sbjct:  346 LDKKQIRAIFLFEFKMGRKAAETTRNINNAFGPGTANERTVQWWFKKFCKGDESLED 402
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BLAST of SMED30028437 vs. TrEMBL
Match: A0A0L7QRG0 (Histone-lysine N-methyltransferase SETMAR OS=Habropoda laboriosa OX=597456 GN=WH47_06699 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.289e-8
Identity = 26/52 (50.00%), Postives = 35/52 (67.31%), Query Frame = 2 
Query:  341 LKNHDLRLFYLYEWKSKNNSVEAERNINNAFGSDTANEGTIRLWF*KIDEGE 496
            +   D R+ +LYEWKS +N+  A RNIN AFG+DT NE  +R WF K + G+
Sbjct:    1 MNQRDFRVIFLYEWKSGHNAAVAARNINAAFGNDTVNERAVRRWFEKFEAGD 52
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BLAST of SMED30028437 vs. TrEMBL
Match: A0A016TST4 (HTH_48 domain-containing protein OS=Ancylostoma ceylanicum OX=53326 GN=Acey_s0082.g1596 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 2.027e-7
Identity = 24/57 (42.11%), Postives = 36/57 (63.16%), Query Frame = 2 
Query:  341 LKNHDLRLFYLYEWKSKNNSVEAERNINNAFGSDTANEGTIRLWF*KIDEGEIYLEN 511
            +   D R+  LYE+K  +++ EA RN+   FG+D+  EGT+R WF KI  G+  LE+
Sbjct:    2 VSRRDFRVIMLYEFKLSHSAAEAARNMALVFGTDSPPEGTVRCWFAKISPGDFDLED 58
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BLAST of SMED30028437 vs. TrEMBL
Match: A0A016TM03 (HTH_48 domain-containing protein OS=Ancylostoma ceylanicum OX=53326 GN=Acey_s0092.g2564 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 4.544e-7
Identity = 24/53 (45.28%), Postives = 35/53 (66.04%), Query Frame = 2 
Query:  353 DLRLFYLYEWKSKNNSVEAERNINNAFGSDTANEGTIRLWF*KIDEGEIYLEN 511
            D R+  LYE+K  +++ EA RNI  AFG+D+ +EGT+R WF K   G+   E+
Sbjct:    6 DFRVIMLYEFKLSHSAAEAARNIALAFGTDSPSEGTVRCWFAKFSSGDFDFED 58
[Close]
BLAST of SMED30028437 vs. TrEMBL
Match: A0A016TF96 (HTH_48 domain-containing protein OS=Ancylostoma ceylanicum OX=53326 GN=Acey_s0108.g49 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 1.167e-6
Identity = 25/57 (43.86%), Postives = 36/57 (63.16%), Query Frame = 2 
Query:  341 LKNHDLRLFYLYEWKSKNNSVEAERNINNAFGSDTANEGTIRLWF*KIDEGEIYLEN 511
            +   D R+  LYE+K  +++ EA RN+  AFGSD+ +E T+R WF KI  G   LE+
Sbjct:    2 VSRRDFRVIMLYEFKLSHSAAEAARNMALAFGSDSPSETTVRCWFAKISSGNFDLED 58
[Close]
BLAST of SMED30028437 vs. TrEMBL
Match: A0A016V6Q7 (HTH_48 domain-containing protein OS=Ancylostoma ceylanicum OX=53326 GN=Acey_s0016.g3034 PE=4 SV=1)

HSP 1 Score: 55.0694 bits (131), Expect = 1.457e-6
Identity = 24/57 (42.11%), Postives = 37/57 (64.91%), Query Frame = 2 
Query:  341 LKNHDLRLFYLYEWKSKNNSVEAERNINNAFGSDTANEGTIRLWF*KIDEGEIYLEN 511
            +   D R+  LYE+K  +++ EA RN+  AFG+D+A+E T+R WF K   G+  LE+
Sbjct:    2 VSRRDFRVIMLYEFKLSHSAAEAARNMALAFGTDSASERTVRCWFAKFSSGDFDLED 58
The following BLAST results are available for this feature:
BLAST of SMED30028437 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 3
Match NameE-valueIdentityDescription
SETMAR3.170e-843.86SET domain and mariner transposase fusion gene [So... [more]
SETMAR4.199e-843.86SET domain and mariner transposase fusion gene [So... [more]
SETMAR4.859e-843.86SET domain and mariner transposase fusion gene [So... [more]
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BLAST of SMED30028437 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 SMED30028437 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 SMED30028437 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 SMED30028437 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 SMED30028437 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 SMED30028437 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q53H47|SETMR_HUMAN2.017e-743.86Histone-lysine N-methyltransferase SETMAR OS=Homo ... [more]
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BLAST of SMED30028437 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0L7QRG01.289e-850.00Histone-lysine N-methyltransferase SETMAR OS=Habro... [more]
A0A016TST42.027e-742.11HTH_48 domain-containing protein OS=Ancylostoma ce... [more]
A0A016TM034.544e-745.28HTH_48 domain-containing protein OS=Ancylostoma ce... [more]
A0A016TF961.167e-643.86HTH_48 domain-containing protein OS=Ancylostoma ce... [more]
A0A016V6Q71.457e-642.11HTH_48 domain-containing protein OS=Ancylostoma ce... [more]
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BLAST of SMED30028437 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 SMED30028437 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 SMED30028437 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 SMED30028437 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 SMED30028437 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 SMED30028437 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

>SMED30028437 ID=SMED30028437|Name=SMED30028437|organism=Schmidtea mediterranea sexual|type=transcript|length=511bp
AGATTTTCAAAAATTATTTGTAGTAACTTTATTAAAAATTTAGTTTATGG
AAAATTGAACCAGAAATTATTTTTTGTTAAAGATTTGTTTTTCCTTAAAA
CGAATTGATTGTGATTAATTCCATTAAATTACGCGGTGGAGTTATTTTCA
TATGTTAGGTTGTCGGAATGAAATGTCCGAATAATATATAATAATTTTAA
ATCATCATAACTTATTATATAAAACTTATTTCTCTATTTTAAAGTTCATT
AGAAAGCGCTTATTTTCAAATTCAAATATTAAGTAAGATTTATAATAATT
TAATTACTATAAATTTCATTTTCAAATAGAAATGTACAAGTTAAAAAATC
ATGATTTGAGACTTTTTTATTTATATGAGTGGAAATCGAAGAATAATTCA
GTTGAGGCGGAGAGGAATATTAATAATGCTTTTGGGAGCGATACAGCTAA
TGAAGGAACTATTAGGCTTTGGTTTTAAAAAATTGATGAGGGAGAAATTT
ATCTCGAAAAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000074oocyte
PLANA:0000231vitelline gland
Vocabulary: INTERPRO
TermDefinition
IPR041426Mos1_HTH
Vocabulary: molecular function
TermDefinition
GO:0008168methyltransferase activity
GO:0016740transferase activity
Vocabulary: biological process
TermDefinition
GO:0032259methylation
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR041426Mos1 transposase, HTH domainPFAMPF17906HTH_48coord: 7..48
e-value: 5.1E-6
score: 26.5