SMED30027740

Overview
NameSMED30027740
Smed IDSMED30027740
Length (bp)1737
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 SMED30027740 (SMED30027740) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027740 (SMED30027740) 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 SMED30027740 (SMED30027740) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027740 (SMED30027740) 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




SMED30027740

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30027740SMESG000045107.1 SmedASXL_009084SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
zeta neoblastSMED30027740SMESG000045107.1 dd_Smed_v4_14425_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30027740SMESG000045107.1 SMED_17283_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30027740SMESG000045107.1 SMED_17283_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30027740SMESG000045107.1 SMED_38037_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30027740SMESG000045107.1 SMED_38037_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027740 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.017611:12456..14298 -6793
v31.001433:120433..123560 -6208
Homology
BLAST of SMED30027740 vs. Planmine SMEST
Match: SMESG000045107.1 (SMESG000045107.1)

HSP 1 Score: 1058.51 bits (2736), Expect = 0.000e+0
Identity = 549/552 (99.46%), Postives = 552/552 (100.00%), Query Frame = 2
Query:   65 MSDIICQTFQSKNRIPLQALSDESMLYGNMIENMNSEIFLKKIKNTFSNINFETIKVIDNKLDYLQELSKNDSNLLEISKVISQYFSIHKQDYWRIYSELRTTILQNDKNSNLYQFKPKSNSLLSIVDIKMEIKEDNSLDKLISNLDLNENLMENVRNHPFXXXXXXXXXVRIYRETATNTDISAENQTTQTESNISDNNFNSTENFLYFYGQTKEINKLVEVLQEKNQTLESKCSQAINQLSSIYQSYKCNFQKINCAKIEFGINTCESWQMNYDKLQSDSLKLVDLTDKLYGAENLIRNYENQIDMLKKENQNQSIKIETLSAENDRLSXXXXXXXXXXXXXRDTNEFLNAEHQSLSAQMEKMQQDWTDSLKTNEERLRQARIDFRKANTKTILEKNDLQFQFNDEKLRSIENQMMVGFTNERIEKVLKDLGNYPLYGTDLEKEVTDLRKKISLMEDKIIEHRHQKEKLRHYQAHMVDKVDARSEVLHKTIATLKATVSELEADNEHVRSLLNKFLKLVEDLRTINLNFENRKAVEYCDSFRTILSKFDV 1720
            MSDIICQTFQSKNRIPLQALS+ESMLYGNMIENMNSEIFLKKIKNTFSNINFETIKVIDNKLDYLQELSKNDSNLLEISKVISQYFSIHKQDYWRIYSELRTTILQNDKNSNLYQFKPKSNSLLSIVDIKMEIKEDNSLDKLISNLDLNENLMENVRNHPFTSSSTSTPSVRIYRETATNTDISAENQTTQTESNISDNNFNST+NFLYFYGQTKEINKLVEVLQEKNQTLESKCSQAINQLSSIYQSYKCNFQKINCAKIEFGINTCESWQMNY+KLQSDSLKLVDLTDKLYGAENLIRNYENQIDMLKKENQNQSIKIETLSAENDRLSQENANIQNEINEIRDTNEFLNAEHQSLSAQMEKMQQDWTDSLKTNEERLRQARIDFRKANTKTILEKNDLQFQFNDEKLRSIENQMMVGFTNERIEKVLKDLGNYPLYGTDLEKEVTDLRKKISLMEDKIIEHRHQKEKLRHYQAHMVDKVDARSEVLHKTIATLKATVSELEADNEHVRSLLNKFLKLVEDLRTINLNFENRKAVEYCDSFRTILSKFDV
Sbjct:    1 MSDIICQTFQSKNRIPLQALSEESMLYGNMIENMNSEIFLKKIKNTFSNINFETIKVIDNKLDYLQELSKNDSNLLEISKVISQYFSIHKQDYWRIYSELRTTILQNDKNSNLYQFKPKSNSLLSIVDIKMEIKEDNSLDKLISNLDLNENLMENVRNHPFTSSSTSTPSVRIYRETATNTDISAENQTTQTESNISDNNFNSTQNFLYFYGQTKEINKLVEVLQEKNQTLESKCSQAINQLSSIYQSYKCNFQKINCAKIEFGINTCESWQMNYEKLQSDSLKLVDLTDKLYGAENLIRNYENQIDMLKKENQNQSIKIETLSAENDRLSQENANIQNEINEIRDTNEFLNAEHQSLSAQMEKMQQDWTDSLKTNEERLRQARIDFRKANTKTILEKNDLQFQFNDEKLRSIENQMMVGFTNERIEKVLKDLGNYPLYGTDLEKEVTDLRKKISLMEDKIIEHRHQKEKLRHYQAHMVDKVDARSEVLHKTIATLKATVSELEADNEHVRSLLNKFLKLVEDLRTINLNFENRKAVEYCDSFRTILSKFDV 552          
BLAST of SMED30027740 vs. Planmine SMEST
Match: SMESG000045107.1 (SMESG000045107.1)

HSP 1 Score: 1012.29 bits (2616), Expect = 0.000e+0
Identity = 531/552 (96.20%), Postives = 534/552 (96.74%), Query Frame = 2
Query:   65 MSDIICQTFQSKNRIPLQALSDESMLYGNMIENMNSEIFLKKIKNTFSNINFETIKVIDNKLDYLQELSKNDSNLLEISKVISQYFSIHKQDYWRIYSELRTTILQNDKNSNLYQFKPKSNSLLSIVDIKMEIKEDNSLDKLISNLDLNENLMENVRNHPFXXXXXXXXXVRIYRETATNTDISAENQTTQTESNISDNNFNSTENFLYFYGQTKEINKLVEVLQEKNQTLESKCSQAINQLSSIYQSYKCNFQKINCAKIEFGINTCESWQMNYDKLQSDSLKLVDLTDKLYGAENLIRNYENQIDMLKKENQNQSIKIETLSAENDRLSXXXXXXXXXXXXXRDTNEFLNAEHQSLSAQMEKMQQDWTDSLKTNEERLRQARIDFRKANTKTILEKNDLQFQFNDEKLRSIENQMMVGFTNERIEKVLKDLGNYPLYGTDLEKEVTDLRKKISLMEDKIIEHRHQKEKLRHYQAHMVDKVDARSEVLHKTIATLKATVSELEADNEHVRSLLNKFLKLVEDLRTINLNFENRKAVEYCDSFRTILSKFDV 1720
            MSDIICQTFQSKNRIPLQALS+ESMLYGNMIENMNSEIFLKKIKNTFSNINFETIKVIDNKLDYLQELSKNDSNLLEISKVISQYFSIHKQDYWRIYSELRTTILQNDKN                  IKMEIKEDNSLDKLISNLDLNENLMENVRNHPFTSSSTSTPSVRIYRETATNTDISAENQTTQTESNISDNNFNST+NFLYFYGQTKEINKLVEVLQEKNQTLESKCSQAINQLSSIYQSYKCNFQKINCAKIEFGINTCESWQMNY+KLQSDSLKLVDLTDKLYGAENLIRNYENQIDMLKKENQNQSIKIETLSAENDRLSQENANIQNEINEIRDTNEFLNAEHQSLSAQMEKMQQDWTDSLKTNEERLRQARIDFRKANTKTILEKNDLQFQFNDEKLRSIENQMMVGFTNERIEKVLKDLGNYPLYGTDLEKEVTDLRKKISLMEDKIIEHRHQKEKLRHYQAHMVDKVDARSEVLHKTIATLKATVSELEADNEHVRSLLNKFLKLVEDLRTINLNFENRKAVEYCDSFRTILSKFDV
Sbjct:    1 MSDIICQTFQSKNRIPLQALSEESMLYGNMIENMNSEIFLKKIKNTFSNINFETIKVIDNKLDYLQELSKNDSNLLEISKVISQYFSIHKQDYWRIYSELRTTILQNDKN------------------IKMEIKEDNSLDKLISNLDLNENLMENVRNHPFTSSSTSTPSVRIYRETATNTDISAENQTTQTESNISDNNFNSTQNFLYFYGQTKEINKLVEVLQEKNQTLESKCSQAINQLSSIYQSYKCNFQKINCAKIEFGINTCESWQMNYEKLQSDSLKLVDLTDKLYGAENLIRNYENQIDMLKKENQNQSIKIETLSAENDRLSQENANIQNEINEIRDTNEFLNAEHQSLSAQMEKMQQDWTDSLKTNEERLRQARIDFRKANTKTILEKNDLQFQFNDEKLRSIENQMMVGFTNERIEKVLKDLGNYPLYGTDLEKEVTDLRKKISLMEDKIIEHRHQKEKLRHYQAHMVDKVDARSEVLHKTIATLKATVSELEADNEHVRSLLNKFLKLVEDLRTINLNFENRKAVEYCDSFRTILSKFDV 534          
The following BLAST results are available for this feature:
BLAST of SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 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 SMED30027740 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000045107.10.000e+099.46SMESG000045107.1[more]
SMESG000045107.10.000e+096.20SMESG000045107.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027740 ID=SMED30027740|Name=SMED30027740|organism=Schmidtea mediterranea sexual|type=transcript|length=1737bp
CCGATCTAATCACGCAAATTTAAAAATTGTTAATTTAAATATTCTTTGTT
TTTAATAGTTTACCATGTCGGATATTATATGCCAGACTTTTCAATCAAAG
AATAGAATTCCACTTCAAGCTTTATCAGATGAATCTATGCTATACGGAAA
TATGATTGAAAACATGAATTCAGAAATTTTTTTAAAGAAAATCAAAAATA
CCTTTAGTAATATAAACTTTGAAACAATTAAAGTGATAGATAATAAACTT
GATTATTTACAAGAATTGTCTAAGAATGATAGCAATTTATTAGAAATTTC
CAAAGTCATTTCTCAATATTTCAGTATTCATAAGCAAGATTATTGGAGAA
TTTATTCAGAATTGCGGACTACGATACTGCAAAATGATAAAAATTCTAAT
TTATATCAATTCAAACCGAAATCAAATTCTCTTCTTTCAATTGTAGACAT
TAAAATGGAAATTAAAGAAGATAATTCACTAGATAAACTCATTAGTAATT
TAGATTTAAATGAAAATTTAATGGAAAACGTAAGAAACCACCCGTTCACC
AGCAGTAGCACAAGCACTCCATCCGTCAGAATATACCGTGAAACGGCGAC
TAACACCGACATTTCCGCCGAAAATCAAACCACTCAAACCGAATCCAATA
TATCGGACAATAATTTCAATAGCACTGAGAATTTTTTATATTTCTACGGC
CAAACCAAAGAAATCAATAAATTAGTAGAAGTTTTGCAAGAGAAAAACCA
AACACTGGAATCAAAATGTTCGCAGGCCATAAATCAATTATCATCGATCT
ATCAATCATACAAGTGCAATTTCCAAAAAATCAATTGTGCAAAAATCGAA
TTTGGCATCAACACGTGTGAAAGCTGGCAAATGAATTACGACAAGCTGCA
GAGTGATAGCTTGAAACTGGTGGACTTGACCGACAAGCTGTATGGCGCTG
AAAACCTCATCAGAAATTATGAGAATCAAATCGATATGTTGAAGAAAGAA
AATCAAAACCAATCGATCAAAATTGAAACCCTATCGGCCGAAAACGATAG
ATTAAGCCAGGAAAACGCTAACATTCAAAACGAAATCAACGAGATCCGCG
ATACGAATGAGTTCTTGAATGCGGAACATCAGAGCTTGTCTGCACAAATG
GAAAAAATGCAACAAGACTGGACGGATTCGTTGAAAACCAATGAGGAGCG
CTTGAGACAAGCCCGGATCGATTTTAGGAAAGCCAACACAAAAACGATTT
TGGAGAAAAACGATTTACAGTTCCAGTTCAACGATGAGAAACTTCGGAGC
ATTGAAAATCAAATGATGGTTGGTTTTACAAATGAGCGGATCGAGAAGGT
GCTGAAGGATTTGGGCAATTACCCGCTGTATGGGACCGATCTGGAGAAGG
AGGTCACCGATCTGAGGAAGAAGATTTCCCTGATGGAGGACAAGATAATC
GAGCATCGGCATCAGAAAGAGAAATTGCGGCATTACCAGGCTCATATGGT
GGATAAGGTCGACGCAAGGAGCGAGGTGTTGCACAAGACCATCGCGACAC
TGAAGGCCACAGTTAGTGAGCTCGAGGCTGACAATGAGCACGTACGGTCA
CTGCTGAATAAATTCCTTAAATTAGTGGAGGATTTGAGGACGATCAATTT
GAATTTCGAAAATAGAAAGGCTGTCGAGTATTGTGATAGTTTCAGAACCA
TTTTATCCAAATTCGATGTATAATTTTTCATAAATAT
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protein sequence of SMED30027740-orf-1

>SMED30027740-orf-1 ID=SMED30027740-orf-1|Name=SMED30027740-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=553bp
MSDIICQTFQSKNRIPLQALSDESMLYGNMIENMNSEIFLKKIKNTFSNI
NFETIKVIDNKLDYLQELSKNDSNLLEISKVISQYFSIHKQDYWRIYSEL
RTTILQNDKNSNLYQFKPKSNSLLSIVDIKMEIKEDNSLDKLISNLDLNE
NLMENVRNHPFTSSSTSTPSVRIYRETATNTDISAENQTTQTESNISDNN
FNSTENFLYFYGQTKEINKLVEVLQEKNQTLESKCSQAINQLSSIYQSYK
CNFQKINCAKIEFGINTCESWQMNYDKLQSDSLKLVDLTDKLYGAENLIR
NYENQIDMLKKENQNQSIKIETLSAENDRLSQENANIQNEINEIRDTNEF
LNAEHQSLSAQMEKMQQDWTDSLKTNEERLRQARIDFRKANTKTILEKND
LQFQFNDEKLRSIENQMMVGFTNERIEKVLKDLGNYPLYGTDLEKEVTDL
RKKISLMEDKIIEHRHQKEKLRHYQAHMVDKVDARSEVLHKTIATLKATV
SELEADNEHVRSLLNKFLKLVEDLRTINLNFENRKAVEYCDSFRTILSKF
DV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000429neoblast
PLANA:0002109X1 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 373..393
NoneNo IPR availableCOILSCoilCoilcoord: 285..368
NoneNo IPR availableCOILSCoilCoilcoord: 440..460
NoneNo IPR availableCOILSCoilCoilcoord: 493..513
NoneNo IPR availableCOILSCoilCoilcoord: 214..241