SMED30016558

Overview
NameSMED30016558
Smed IDSMED30016558
Length (bp)1170
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 SMED30016558 (SMED30016558) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016558 (SMED30016558) 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 SMED30016558 (SMED30016558) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016558 (SMED30016558) 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



SMED30016558

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
X1 cellSMED30016558SMESG000041125.1 SmedASXL_002145SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30016558 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000396:140631..141800 -5814
Homology
[Close]
BLAST of SMED30016558 vs. TrEMBL
Match: A0A183AZN6 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS12420 PE=4 SV=1)

HSP 1 Score: 66.6254 bits (161), Expect = 1.812e-8
Identity = 56/226 (24.78%), Postives = 104/226 (46.02%), Query Frame = 1 
Query:  487 VTEIYQIGF--QVGDT---ERIYLPNILDFQDVSYQYRSDIQLCEDTVNAIWNDMTPMILSQDYQKEYKGIQQQSMEQLENYLATNLSNIIAKSRLQEKQSM---LISHKRIVELRKNMFHMLSKIFSELKFSPKFNPISQDIDRLIDHFIIVQSCCLASNREEYIKLIQTIPDRDSLDPVVVLCKDLNMYYKELQQKCLKLIKLFIPQLELPSEFSISKDLNELI 1140
            V E YQ+G+     DT   ER+Y+ + +D  +V+Y          DT+ A   D+ P+ L  +Y  +   +   ++ QL   LA  L   IA+ R QE++ M   + +H+  V LRK +  ++ ++          +  S   D+ +   I V +        + ++ + T    +   P+V LC D       L+ +  +L+++ +P L LP  F + +DL+ L+
Sbjct:  113 VHETYQLGYFDPTSDTDLLERLYVFDFVDGLEVTYPISVT---SSDTLPA---DLPPLFLEPEYVDQLSTLASNALNQLTTVLANWL---IARQRSQEERLMWHHMSAHEEAVLLRKQVVQLIDQLVPTSHLESTLDFHSPLTDKFLTQLISVLT-------RDTMEKVSTNNASEGAIPIVSLCPDPTHCLNALRTQIYQLLRILVPHLRLPQSFHLERDLHSLL 322
[Close]
BLAST of SMED30016558 vs. TrEMBL
Match: A0A5K3FXQ0 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.570e-7
Identity = 52/229 (22.71%), Postives = 100/229 (43.67%), Query Frame = 1 
Query:  487 VTEIYQIGFQVGDTERIYLPNILDFQDVSYQYRSDIQLCEDTVNAIWND----MTPMILSQDYQKEYKGIQQQSMEQLENYLATNLSNIIAKSRLQEKQSMLISHKRIVELRKNMFHMLSKIFSELKFSPKFNPISQDIDRLIDHFIIVQSCCLASNREEYIKLIQTIPDRDSLDPVVVLCKDLNMYYKELQQKCLKLIKLFIPQLELPSEFSISKDLNELIQRISTVN 1161
            V EIYQ+G +  +   IYL + +D   VSY           T++ +  D    + P    + + +    +      QL + L T +  + A ++ +     + +H+ +  LR+ +F +L  +      S  F+  + D+DRL+             +         T  D +   P+V +C +     + L+Q+ L L++  +P L LP  F I++DL++LI  + + N
Sbjct:   72 VDEIYQLGIEHKENNEIYLFDFVDSLQVSYPV---------TLSHVSTDRLEKLPPYFHGRLFDEHLSCLASDVFRQLTSRLETWMDALDANAQTEFIARHMKAHEELTILRRQIFTLLKLLVPNPSLSDGFDCTTADLDRLL---------VRIISEISKSGSSSTDGDENLSLPIVSVCIEPEHCVQVLRQRVLTLLQTLLPSLRLPKSFDITRDLHDLINAVYSYN 282
[Close]
BLAST of SMED30016558 vs. TrEMBL
Match: A0A5K3FWZ9 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.966e-7
Identity = 51/225 (22.67%), Postives = 100/225 (44.44%), Query Frame = 1 
Query:  487 VTEIYQIGFQVGDTERIYLPNILDFQDVSYQYRSDIQLCEDTVNAIWNDMTPMILSQDYQKEYKGIQQQSMEQLENYLATNLSNIIAKSRLQEKQSMLISHKRIVELRKNMFHMLSKIFSELKFSPKFNPISQDIDRLIDHFIIVQSCCLASNREEYIKLIQTIPDRDSLDPVVVLCKDLNMYYKELQQKCLKLIKLFIPQLELPSEFSISKDLNELIQRISTVN 1161
            V EIYQ+G +  +   IYL + +D   VSY     + L   + + +   + P    + + +    +      QL + L T +  + A ++ +     + +H+ +  LR+ +F +L  +      S  F+  + D+DRL+             +         T  D +   P+V +C +     + L+Q+ L L++  +P L LP  F I++DL++LI  + + N
Sbjct:  107 VDEIYQLGIEHKENNEIYLFDFVDSLQVSYP----VTLSHVSTDRL-EKLPPYFHGRLFDEHLSCLASDVFRQLTSRLETWMDALDANAQTEFIARHMKAHEELTILRRQIFTLLKLLVPNPSLSDGFDCTTADLDRLL---------VRIISEISKSGSSSTDGDENLSLPIVSVCIEPEHCVQVLRQRVLTLLQTLLPSLRLPKSFDITRDLHDLINAVYSYN 317
[Close]
BLAST of SMED30016558 vs. TrEMBL
Match: A0A0R3UBG6 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS4267 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 1.851e-6
Identity = 53/227 (23.35%), Postives = 106/227 (46.70%), Query Frame = 1 
Query:  487 VTEIYQIGFQVGDTERIYLPNILDFQDVSYQYRSDIQLCEDTVNAIWNDMTPMILSQDYQKEYKGIQQQSMEQLENYLATNLSNIIAKSRLQEKQSMLISHKRIVELRKNMFHMLSKIFSELKFSPKFNPISQDIDRLI--DHFIIVQSCCLASNREEYIKLIQTIPDRDSLDPVVVLCKDLNMYYKELQQKCLKLIKLFIPQLELPSEFSISKDLNELIQRISTVN 1161
            V EIYQ+G +  +   IYL + +D   VSY     + L   + + +   + P    + + +    +      QL + L T +  + A ++ +     + +H+ +  LR+ +F +L  +      S  F+  + D+DRL+      I +S   +++ +E + L           P+V +C +     + L+Q+ L L++  +P L LP  F I++DL++LI  + + N
Sbjct:  494 VDEIYQLGIEHKENNEIYLFDFVDSLQVSYP----VTLSHVSTDRL-EKLPPYFHGRLFDEHLSCLASDVFRQLTSRLETWMDALDANAQTEFIARHMKAHEELTILRRQIFTLLKLLVPNPSLSDGFDCTTADLDRLLVRIISEISKSGSSSTDGDENLSL-----------PIVSVCIEPEHCVQVLRQRVLTLLQTLLPSLRLPKSFDITRDLHDLINAVYSYN 704
[Close]
BLAST of SMED30016558 vs. TrEMBL
Match: A0A5J4N6L2 (Uncharacterized protein OS=Paragonimus westermani OX=34504 GN=DEA37_0008671 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 4.371e-6
Identity = 71/278 (25.54%), Postives = 119/278 (42.81%), Query Frame = 1 
Query:  361 ESMTTSDSPFAESLNSNLCATDDVLAF--EYVTSMDLPKKYEYKVTEIYQIGF---QVGDTE--RIYLPNILDFQDVSYQYRSDIQLCEDTVNAIWNDMTPMILSQDYQKEYKGIQQQSMEQLENYLATNLSNIIAKSRLQEKQSMLI----SHKRIVELRKNMFHMLSKIFSELKFSPKFNPISQDIDRLIDHFIIVQSCCLASNREEYIKLIQTIPDRDSLDPVVVLCKDLNMYYKELQQKCLKLIKLFIPQLELPSEFSISKDLNELIQRISTVN 1161
            +S +TS S   + L S LC + D   F  E+  + +        V E YQ+G+     G+T+   +Y+ + +D  +VSY             +A+  D+ P+ +  DY  +   +   ++ QL    A  L+N     +  ++Q  +     +H+   ELRK     L+ +   L     F   S  +D L+           A N + + K +      D L PVV LC D       L+ + + L++  +PQLELP  F  S+DL  L+  +  VN
Sbjct:   86 QSKSTSLSTEFDHLASGLCTSVDSQRFIEEFQCNEE---TVTISVQETYQLGYCDPTSGNTDCGNLYVFDFVDGIEVSYPVSVTAS------DALPLDLPPLFIEPDYVDQLTSLATSALTQL----AQLLNNWFLSCQSADEQLFVWRHMQAHEEATELRKKAIKFLASLVPALGNRWDFQ--SPRVDTLLTQLTS------ALNVDTFGKRVDA-QQTDKLVPVVSLCSDPYHCLNLLRSQIVALLQKLLPQLELPQSFDSSRDLQPLLATLCEVN 341
[Close]
BLAST of SMED30016558 vs. Planmine SMEST
Match: SMESG000041125.1 (SMESG000041125.1)

HSP 1 Score: 667.922 bits (1722), Expect = 0.000e+0
Identity = 327/327 (100.00%), Postives = 327/327 (100.00%), Query Frame = 1 
Query:  181 MNGGLKVSETNNNNYKSLKRKSNSFYENFKSKVVKVSKLEIENSFEHHLNMNKTNDSYVTESMTTSDSPFAESLNSNLCATDDVLAFEYVTSMDLPKKYEYKVTEIYQIGFQVGDTERIYLPNILDFQDVSYQYRSDIQLCEDTVNAIWNDMTPMILSQDYQKEYKGIQQQSMEQLENYLATNLSNIIAKSRLQEKQSMLISHKRIVELRKNMFHMLSKIFSELKFSPKFNPISQDIDRLIDHFIIVQSCCLASNREEYIKLIQTIPDRDSLDPVVVLCKDLNMYYKELQQKCLKLIKLFIPQLELPSEFSISKDLNELIQRISTVN 1161
            MNGGLKVSETNNNNYKSLKRKSNSFYENFKSKVVKVSKLEIENSFEHHLNMNKTNDSYVTESMTTSDSPFAESLNSNLCATDDVLAFEYVTSMDLPKKYEYKVTEIYQIGFQVGDTERIYLPNILDFQDVSYQYRSDIQLCEDTVNAIWNDMTPMILSQDYQKEYKGIQQQSMEQLENYLATNLSNIIAKSRLQEKQSMLISHKRIVELRKNMFHMLSKIFSELKFSPKFNPISQDIDRLIDHFIIVQSCCLASNREEYIKLIQTIPDRDSLDPVVVLCKDLNMYYKELQQKCLKLIKLFIPQLELPSEFSISKDLNELIQRISTVN
Sbjct:    1 MNGGLKVSETNNNNYKSLKRKSNSFYENFKSKVVKVSKLEIENSFEHHLNMNKTNDSYVTESMTTSDSPFAESLNSNLCATDDVLAFEYVTSMDLPKKYEYKVTEIYQIGFQVGDTERIYLPNILDFQDVSYQYRSDIQLCEDTVNAIWNDMTPMILSQDYQKEYKGIQQQSMEQLENYLATNLSNIIAKSRLQEKQSMLISHKRIVELRKNMFHMLSKIFSELKFSPKFNPISQDIDRLIDHFIIVQSCCLASNREEYIKLIQTIPDRDSLDPVVVLCKDLNMYYKELQQKCLKLIKLFIPQLELPSEFSISKDLNELIQRISTVN 327
The following BLAST results are available for this feature:
BLAST of SMED30016558 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 SMED30016558 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 SMED30016558 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 SMED30016558 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 SMED30016558 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 SMED30016558 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 SMED30016558 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 SMED30016558 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183AZN61.812e-824.78Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A5K3FXQ01.570e-722.71Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A5K3FWZ91.966e-722.67Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A0R3UBG61.851e-623.35Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A5J4N6L24.371e-625.54Uncharacterized protein OS=Paragonimus westermani ... [more]
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BLAST of SMED30016558 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 SMED30016558 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 SMED30016558 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 SMED30016558 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 SMED30016558 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 SMED30016558 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000041125.10.000e+0100.00SMESG000041125.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016558 ID=SMED30016558|Name=SMED30016558|organism=Schmidtea mediterranea sexual|type=transcript|length=1170bp
TAAAGTTTTAAATGGTAAAAAATTATAGGCTTTAAAATTAATTAACCAAT
AGATTTTTAATTATAATTTTAATAGAAAACATGATAAATTTGTTTTAAAA
TATAATACAGTTTGTTAAATTGAAAGAAAACAATTTTTTATATTTTTCTG
TTGAATTATAATAAAGTGTTCAAATTTAATATGAATGGTGGATTAAAGGT
TTCTGAAACCAATAACAACAATTACAAATCATTAAAAAGAAAGTCTAATT
CCTTTTATGAAAACTTCAAATCCAAAGTGGTCAAAGTTAGCAAATTAGAA
ATTGAAAATTCCTTTGAACATCATCTAAATATGAATAAAACAAATGATAG
TTATGTTACAGAAAGCATGACAACTTCTGATTCTCCATTTGCCGAATCTC
TTAATTCCAATTTATGTGCTACAGATGATGTTTTGGCTTTTGAGTATGTT
ACTTCAATGGATCTTCCAAAAAAATATGAATATAAAGTAACTGAAATTTA
TCAAATTGGATTTCAAGTGGGTGATACCGAAAGAATTTATTTACCAAATA
TTTTGGACTTTCAAGATGTTTCTTATCAATACCGTTCTGATATACAACTA
TGTGAGGATACGGTAAATGCAATTTGGAATGATATGACTCCAATGATTTT
AAGTCAAGACTATCAAAAAGAATATAAAGGTATACAGCAACAAAGTATGG
AACAATTAGAAAATTATTTAGCTACTAATTTATCAAATATCATTGCTAAA
TCCAGATTACAGGAAAAACAGTCTATGCTGATTTCTCATAAACGAATAGT
GGAATTACGCAAAAATATGTTTCATATGCTTTCTAAAATATTTTCTGAAT
TAAAATTTTCCCCGAAATTTAATCCTATATCCCAAGATATTGATAGATTA
ATAGATCATTTTATAATTGTCCAATCTTGTTGTTTGGCATCGAATCGTGA
AGAATATATAAAATTAATTCAGACAATTCCAGATCGTGATTCTTTGGATC
CTGTCGTTGTTCTCTGTAAGGATTTAAATATGTATTATAAAGAATTGCAG
CAAAAATGTCTCAAATTGATCAAACTATTTATACCACAACTGGAATTACC
TTCGGAGTTCAGTATCAGCAAAGATTTAAATGAATTGATTCAAAGAATTT
CTACAGTTAATTGATTTGTA
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protein sequence of SMED30016558-orf-1

>SMED30016558-orf-1 ID=SMED30016558-orf-1|Name=SMED30016558-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=328bp
MNGGLKVSETNNNNYKSLKRKSNSFYENFKSKVVKVSKLEIENSFEHHLN
MNKTNDSYVTESMTTSDSPFAESLNSNLCATDDVLAFEYVTSMDLPKKYE
YKVTEIYQIGFQVGDTERIYLPNILDFQDVSYQYRSDIQLCEDTVNAIWN
DMTPMILSQDYQKEYKGIQQQSMEQLENYLATNLSNIIAKSRLQEKQSML
ISHKRIVELRKNMFHMLSKIFSELKFSPKFNPISQDIDRLIDHFIIVQSC
CLASNREEYIKLIQTIPDRDSLDPVVVLCKDLNMYYKELQQKCLKLIKLF
IPQLELPSEFSISKDLNELIQRISTVN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell