SMED30027026

Overview
NameSMED30027026
Smed IDSMED30027026
Length (bp)805
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 SMED30027026 (SMED30027026) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027026 (SMED30027026) 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



SMED30027026

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
zeta neoblastSMED30027026 dd_Smed_v4_18426_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
SMED30027026 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006085:3695..4603 -3960
Homology
[Close]
BLAST of SMED30027026 vs. TrEMBL
Match: A0A0C2M816 (DDE_Tnp_IS1595 domain-containing protein OS=Thelohanellus kitauei OX=669202 GN=RF11_01854 PE=4 SV=1)

HSP 1 Score: 47.3654 bits (111), Expect = 7.352e-10
Identity = 27/72 (37.50%), Postives = 40/72 (55.56%), Query Frame = -2 
Query:    4 PYV-QWVNHSENFIDPITCVNTNAIEGFWALCSNYMFR---TRSNFVPSYVD*FIWRRRFCSN-EQTFDVLM 204
            PY+ + VNH+  F DPIT  +TN +E +WA       R   T SN +   +D  +WR R+    E+TF+ +M
Sbjct:  145 PYIHRTVNHTLFFRDPITGAHTNNVEAYWASVKKSFKRGGQTSSNLLQQKIDEKMWRERYGKTPEETFENIM 216

HSP 2 Score: 45.0542 bits (105), Expect = 7.352e-10
Identity = 27/72 (37.50%), Postives = 38/72 (52.78%), Query Frame = -1 
Query:  239 IASWKLVSESLIFGGENCLVQVDESKFMNVLHNRVESRGNTCAGWLFGIIDSSTKNVNS*KIGHNFGLMNMK 454
            I SWKL ++SLI GG   +VQ+DES     +HNR          W+ G+ D+++      KIG   G+ N K
Sbjct:   44 ICSWKLSTQSLILGGPGHIVQIDESVISRAMHNRGHDLLRP-QRWVLGMYDAAS------KIGIIVGIPNRK 108
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BLAST of SMED30027026 vs. TrEMBL
Match: A0A059EQK9 (DDE_Tnp_IS1595 domain-containing protein (Fragment) OS=Anncaliia algerae PRA109 OX=1240240 GN=H311_01670 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 1.290e-8
Identity = 33/68 (48.53%), Postives = 43/68 (63.24%), Query Frame = -2 
Query:   19 LRPYVQWV-NHSENFIDPITCVNTNAIEGFWALCS---NYMFRTRSNFVPSYVD*FIWRRRFCSNEQT 210
            L PY  +V NHS N+ DPIT V+TN IE FW         M+ T+ +FVPSY+D F+WR R+  +E T
Sbjct:   64 LGPYNHYVVNHSVNYKDPITGVHTNNIEAFWNSAKRKFKQMYGTKIDFVPSYLDEFMWRNRYILSEDT 131
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BLAST of SMED30027026 vs. TrEMBL
Match: A0A059EX22 (DDE_Tnp_IS1595 domain-containing protein OS=Anncaliia algerae PRA339 OX=1288291 GN=H312_03188 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 2.124e-8
Identity = 33/73 (45.21%), Postives = 43/73 (58.90%), Query Frame = -2 
Query:   19 TSFTRLRPYVQWV-NHSENFIDPITCVNTNAIEGFWALCS---NYMFRTRSNFVPSYVD*FIWRRRFCSNEQT 225
            T    L PY  +V NHS N+ DPIT V+TN IE FW         M+ T+  FVP Y+D F+WR+R+  +E T
Sbjct:   52 TPLALLGPYNHYVVNHSVNYKDPITGVHTNNIEAFWNSAKRKFKQMYGTKIEFVPRYLDEFMWRKRYNLSEDT 124
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BLAST of SMED30027026 vs. TrEMBL
Match: A0A2P8XE21 (DDE_Tnp_IS1595 domain-containing protein (Fragment) OS=Blattella germanica OX=6973 GN=C0J52_28262 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.232e-7
Identity = 24/66 (36.36%), Postives = 42/66 (63.64%), Query Frame = -2 
Query:    1 VNHSENFIDPITCVNTNAIEGFWALCSNYMFRT---RSNFVPSYVD*FIWRRRFCSNEQTFDVLMD 189
            VNH +NF+DP T   TNA+EG+WA    ++ +T   +S  +P ++D F+WR  +C ++  F  +++
Sbjct:   98 VNHKDNFVDPTTGACTNAVEGYWAKLKRFLRQTDTMKSRLLPEHIDEFMWRDAYCEDDNVFKKIIE 163
[Close]
BLAST of SMED30027026 vs. TrEMBL
Match: A0A2P8XTX1 (DDE_Tnp_IS1595 domain-containing protein OS=Blattella germanica OX=6973 GN=C0J52_06616 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 7.993e-7
Identity = 22/59 (37.29%), Postives = 38/59 (64.41%), Query Frame = -2 
Query:   22 VNHSENFIDPITCVNTNAIEGFWALCSNYMFRT---RSNFVPSYVD*FIWRRRFCSNEQ 189
            VNH ++F+DP T   TNA+EG+W+    ++ +T   +S  +P ++D F+WR  +C + Q
Sbjct:  122 VNHKDHFVDPTTGACTNAVEGYWSKLKGFLRQTNTLKSTLLPEHIDEFMWREAYCQDAQ 180
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BLAST of SMED30027026 vs. Ensembl Nematostella
Match: EDO42125 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S2D7])

HSP 1 Score: 36.1946 bits (82), Expect = 5.144e-6
Identity = 22/61 (36.07%), Postives = 30/61 (49.18%), Query Frame = -2 
Query:   16 VNHSENFIDPITCVNTNAIEGFWALCSNYMFRTRS---NFVPSYVD*FIWRRRFCSNEQTF 189
            V H  NF+DPIT V++  IE  W+   + +   R      + SY+D   WR    SN  TF
Sbjct:   67 VVHRYNFVDPITGVHSQHIESLWSRLKSTVKERRGIRRVHLQSYLDEQTWRDWRASNRGTF 127

HSP 2 Score: 30.8018 bits (68), Expect = 5.144e-6
Identity = 19/54 (35.19%), Postives = 28/54 (51.85%), Query Frame = -1 
Query:  305 QDIASWKLVSESLI-FGGENCLVQVDESKF-MNVLHNRVESRGNTCAGWLFGII 460
            +DI +  L    +I FGG   + Q+DES+F     HNR   R      W+FG++
Sbjct:   17 RDICAEDLRRRPVIPFGGPGVVCQIDESRFNHKPKHNR--GRPPMRENWVFGVV 68
[Close]
BLAST of SMED30027026 vs. Ensembl Nematostella
Match: EDO42124 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S2D6])

HSP 1 Score: 36.5798 bits (83), Expect = 5.208e-6
Identity = 22/61 (36.07%), Postives = 30/61 (49.18%), Query Frame = -2 
Query:   16 VNHSENFIDPITCVNTNAIEGFWALCSNYMFRTRS---NFVPSYVD*FIWRRRFCSNEQTF 189
            V H  NF+DPIT V++  IE  W+   + +   R      + SY+D   WR    SN  TF
Sbjct:  222 VVHRYNFVDPITGVHSQHIESLWSRLKSTVKERRGIRRVHLQSYLDEQTWRDWRASNRGTF 282

HSP 2 Score: 30.4166 bits (67), Expect = 5.208e-6
Identity = 19/54 (35.19%), Postives = 28/54 (51.85%), Query Frame = -1 
Query:  305 QDIASWKLVSESLI-FGGENCLVQVDESKF-MNVLHNRVESRGNTCAGWLFGII 460
            +DI +  L    +I FGG   + Q+DES+F     HNR   R      W+FG++
Sbjct:  172 RDICAEDLRRRPVIPFGGPGVVCQIDESRFNHKPKHNR--GRPPMRENWVFGVV 223
The following BLAST results are available for this feature:
BLAST of SMED30027026 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 SMED30027026 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 SMED30027026 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 SMED30027026 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 SMED30027026 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 SMED30027026 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 SMED30027026 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 SMED30027026 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0C2M8167.352e-1037.50DDE_Tnp_IS1595 domain-containing protein OS=Theloh... [more]
A0A059EQK91.290e-848.53DDE_Tnp_IS1595 domain-containing protein (Fragment... [more]
A0A059EX222.124e-845.21DDE_Tnp_IS1595 domain-containing protein OS=Anncal... [more]
A0A2P8XE211.232e-736.36DDE_Tnp_IS1595 domain-containing protein (Fragment... [more]
A0A2P8XTX17.993e-737.29DDE_Tnp_IS1595 domain-containing protein OS=Blatte... [more]
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BLAST of SMED30027026 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 SMED30027026 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 SMED30027026 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 SMED30027026 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 2
Match NameE-valueIdentityDescription
EDO421255.144e-636.07Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO421245.208e-636.07Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30027026 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 SMED30027026 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

>SMED30027026 ID=SMED30027026|Name=SMED30027026|organism=Schmidtea mediterranea sexual|type=transcript|length=805bp
ATCCATTAATACGTCAAATGTTTGTTCATTGCTGCAAAATCTTCTCCTCC
AAATAAATTAATCTACATAAGAAGGTACGAAGTTACTCCTCGTTCGAAAC
ATGTAATTTGAACATAGGGCCCAAAAACCTTCGATTGCATTGGTGTTCAC
ACAAGTTATTGGATCAATGAAATTTTCTGAATGATTTACCCATTGAACAT
ATGGTCGTAGTCTTGTAAAGGATGTTGGTTCTTCGGTGTTTCATATTCAT
GAGACCAAAGTTGTGTCCTATCTTCTACGAATTCACGTTTTTGGTAGAAC
TGTCAATAATCCCAAATAACCAACCCGCGCATGTATTTCCTCTTGATTCA
ACGCGATTATGTAGTACGTTCATGAATTTTGATTCATCCACTTGCACTAG
ACAGTTTTCACCACCAAAAATCAAAGACTCAGAAACTAATTTCCAACTTG
CGATATCTTGTTTAATCGAGCATTTTGCTCCTCAGAAAAGCATTAGCAAA
AATAGATCTTGAATATGTAAGTTGGAAAAAACTACCGGATGTTATAGTTT
GTTTTACCGGATGGGAATTTATTTGAGACCTGCTTCTGCAAGCAAAGATG
TACTAGTTAAGTACGCTTGGATCTTTCACGAGTTTCATTGTACGCCAACA
TTTTATACATGTAGGAGTAGGGTGCAAAAAANCCCACTTCTTGAAAATGG
CAAATTAGATTGGTAGTATCTCGTGCCAGTTCATATATTTCATTCGATTT
CATGGTTGATAAATAATAGTATAAATATCAATAAATTCATTTATTTCTAA
TTTAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast