SMED30024487

Overview
NameSMED30024487
Smed IDSMED30024487
Length (bp)1073
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 SMED30024487 (SMED30024487) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024487 (SMED30024487) 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 SMED30024487 (SMED30024487) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024487 (SMED30024487) 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




SMED30024487

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
cephalic gangliaSMED30024487SMESG000035432.1 dd_Smed_v4_4853_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30024487SMESG000035432.1 dd_Smed_v4_4853_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30024487 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004395:55990..57062 -5195
v31.004395:64554..65588 -4612
Homology
BLAST of SMED30024487 vs. Planmine SMEST
Match: SMESG000035432.1 (SMESG000035432.1)

HSP 1 Score: 442.195 bits (1136), Expect = 3.614e-157
Identity = 212/220 (96.36%), Postives = 216/220 (98.18%), Query Frame = 1
Query:  223 FTDGSCGDLECYVDRISNTRYVNCSRGHDPHSKTFICQYNEDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLGKIKDLSINYIQVKYIKKSDFLSLFNARYLEMSIPMEIDEDSFIPFNSSFFEISMKCNNDSSNLQFKLQIEKWRIYLHYCNYRAACSLVSSGEKYEYNIQLNHEGKYTPTTVTITNENCSQLLPTKIYFTTTRPSEISTNYSTQSRE 882
            FTDGSCGDLECYVDRISNT+YVNCSR HDPHSKTF CQYNEDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLGKIKDLSINYIQVKYIKKSDFL+LFNARYLEMSIPMEIDEDSFIPFNSSFFEISMKCNNDSSNLQFKLQIEKWRIYLHYCNYRAACSLV SGEKYEYNIQLNH+GKYTPTTVTITNENCS+LLPTKIYFTTTRPSEISTNYSTQS E
Sbjct:   19 FTDGSCGDLECYVDRISNTQYVNCSREHDPHSKTFECQYNEDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLGKIKDLSINYIQVKYIKKSDFLTLFNARYLEMSIPMEIDEDSFIPFNSSFFEISMKCNNDSSNLQFKLQIEKWRIYLHYCNYRAACSLVRSGEKYEYNIQLNHDGKYTPTTVTITNENCSRLLPTKIYFTTTRPSEISTNYSTQSSE 238          

HSP 2 Score: 49.6766 bits (117), Expect = 1.290e-6
Identity = 25/28 (89.29%), Postives = 27/28 (96.43%), Query Frame = 3
Query:  900 HFSFLYINISVVMLMMIIGFAIYIKRNL 983
            +FSFLYINISVV+LMMIIGFAIYI RNL
Sbjct:  245 NFSFLYINISVVLLMMIIGFAIYIIRNL 272          
BLAST of SMED30024487 vs. Planmine SMEST
Match: SMESG000035449.1 (SMESG000035449.1)

HSP 1 Score: 179.874 bits (455), Expect = 4.904e-54
Identity = 94/208 (45.19%), Postives = 129/208 (62.02%), Query Frame = 1
Query:  238 CGDLECYVDRISNTRYVNCSRGHDPHSKTFICQYNEDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLGKIKDLSINYIQVKYIKKSDFLSLFNARYLEMSIPMEIDEDSFIPFNSSFFEISMKCNNDSSNLQFKLQIEKWRIYLHYCNYRAACSLVSSGEKYEYNIQLNHEGKYTPTTVTITNENCSQLLPTKIYFTTTRPSEISTN 861
            C +  CY+D  + TRYVNC+  +  +  + IC+Y  D++ LKLKN +  +   ++FA+ LF N+QK+LG+I  L +  + VKY K+SDFL L + + L++  PM I EDSF PFN S  ++ M C   SSNL FKLQ++ W IYL  CNY   CS   SG KYEYNIQL  + +       ITN+NC+Q + TK  F TT   +I TN
Sbjct:   36 CSNTRCYIDETNATRYVNCTHENVQNGTSLICEY--DDEVLKLKNLNFTIGLAEEFANNLFGNLQKNLGRITKLKMENLNVKYFKRSDFLGLPDLKLLQIITPMAIKEDSFKPFNGSQLKMYMNCKLYSSNLHFKLQVQIWAIYLTNCNYSLICSYFVSGAKYEYNIQLYEKNQIPKGKDPITNDNCTQKVSTKNTFQTTSQYKIKTN 241          
BLAST of SMED30024487 vs. Planmine SMEST
Match: SMESG000035443.1 (SMESG000035443.1)

HSP 1 Score: 177.563 bits (449), Expect = 2.603e-53
Identity = 90/189 (47.62%), Postives = 122/189 (64.55%), Query Frame = 1
Query:  238 CGDLECYVDRISNTRYVNCSRGHDPHSKTFICQYNEDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLGKIKDLSINYIQVKYIKKSDFLSLFNARYLEMSIPMEIDEDSFIPFNSSFFEISMKCNNDSSNLQFKLQIEKWRIYLHYCNYRAACSLVSSGEKYEYNIQLNHEGKYTPTTVTITNENCSQ 804
            C +  CY+D  +  RYV CS G+        C+Y+  +KSL L++ ++ +K+ D+FA  LFE ++   G I+ L+I  IQV YIKKSDF SLFN  YL ++ PM IDEDSF     SFFEISMKCN+ SS+ +F L+ +KW+I LH CNYR  CS   SGE+YEYNI L+++ KY      I+N  C +
Sbjct:   26 CRNTRCYIDGTNTARYVTCSHGNVQRRSLLKCEYDNMDKSLTLRSPENNMKTADRFADHLFEILETSFGPIEKLTIENIQVNYIKKSDFSSLFNLTYLNIATPMIIDEDSFTSTFRSFFEISMKCNSISSSFRFNLK-KKWKIILHECNYRFECSSAGSGEQYEYNIHLSNDVKYYLDLAVISNAGCEK 213          
BLAST of SMED30024487 vs. Planmine SMEST
Match: SMESG000035450.1 (SMESG000035450.1)

HSP 1 Score: 82.4185 bits (202), Expect = 2.335e-17
Identity = 60/230 (26.09%), Postives = 113/230 (49.13%), Query Frame = 1
Query:  238 CGDLECYVDRISNTRYVNCS----RGHDPHSKTFICQYNEDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLGKIKDLSINYIQVKYIKKSDFLSLFNARYLEMSIPMEIDEDSFIP-FNSSFFEISMKCNND---SSNL-QFKLQIEKWRIYLHYCNYRAACSL------VSSGEKYEYNIQLNHEGKYTPTTV---TITNENCSQLLPTKIYFTTTR-----PSEIST 858
            C D++C+++   + R + C       +  + K   C+Y+   K+L +K       SVD   +G F+   + L +I +L I ++++  I +SDF+ L   R L +  P  ++EDSF+   NS +F++ + CNN+   SS + + ++  + WRI L  C Y   C+L      V  G +Y+   QL ++   + + +   T    N   + PT   + +++     P ++ST
Sbjct:   30 CEDIDCFIETDLSARVLGCDYKVLLANKTNLKFLKCEYDLKRKALFIKPLTAGDNSVDGLLTGGFKVFSESLKEITELHIPHVKINNISRSDFVGLEKLRGLTLMNPGNLEEDSFLDIINSEYFQLYIYCNNEKNHSSGISKLRISSKSWRIVLRDCRYSFGCNLGTCVNGVRIGNEYQVKFQLRNKSPESESVIRSSTCLKSNIHCVKPTTTMWPSSKSDMIIPLQVST 259          
BLAST of SMED30024487 vs. Planmine SMEST
Match: SMESG000035431.1 (SMESG000035431.1)

HSP 1 Score: 67.781 bits (164), Expect = 3.159e-12
Identity = 55/200 (27.50%), Postives = 101/200 (50.50%), Query Frame = 1
Query:  250 ECYVDRISNTRYVNCSRGHDPHSKTFICQYN--EDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLGKIKDLSINYIQVKYIKKSDFLSLFNARYLEMSIPMEIDEDSFIPF-NSSFFEISMKCNND----------SSNLQFKLQIEKWRIYLHYCNYRAACSL----VSSGEKYEYNIQLNHEGKYTPTTVTITNENC 798
            EC+VD ISN + +NC       +++ + + N   D + L   +    +  VD+F+  +F+ I+ +L KIK + +++I+V +I++SD   L N + L ++ P   D DSF+   +S  F++ + C  +          S++L F      WR+    C +R  C +     +SG K ++ ++LN E     T V + + NC
Sbjct:   26 ECFVD-ISN-QSLNCGNETVNRNQSKMRRINCALDREELTFSHNYPGMVIVDRFSDQMFQTIKLNLSKIKAVRLSHIKVNHIRRSDLKYLSNIKSLTIANPKTFDIDSFLDIRHSDLFQLYIYCGTEIPKNYSSDYNSTSLSFLFHFTNWRVIQINCLHRYQCEIEECVKNSGIKSKFFLKLNREKISNDTEVYLKSNNC 223          
The following BLAST results are available for this feature:
BLAST of SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 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 SMED30024487 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000035432.13.614e-15796.36SMESG000035432.1[more]
SMESG000035449.14.904e-5445.19SMESG000035449.1[more]
SMESG000035443.12.603e-5347.62SMESG000035443.1[more]
SMESG000035450.12.335e-1726.09SMESG000035450.1[more]
SMESG000035431.13.159e-1227.50SMESG000035431.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024487 ID=SMED30024487|Name=SMED30024487|organism=Schmidtea mediterranea sexual|type=transcript|length=1073bp
ATTTATTCGTGTTCAATAGCCGCCGTTTTGTTGCACAATAAATATCCGGT
TTAGAATAATTTTATTTTAGAAATTTATTACGATAATTATAATAAGGATG
TTCAGTTTCATTGTGACGTCAAATCAGGTTTGTCTCGTCATTCCATGATT
CGCTTCAGACTCGCATTAATGTCGGTTATAATAATTATAAAAATAATAAT
ATTATCGATAATTATTCCAATATTCACAGACGGATCTTGTGGAGATTTAG
AATGCTATGTCGATAGGATCAGCAATACTCGATATGTGAATTGCTCCCGT
GGACATGATCCACATAGCAAGACATTTATATGCCAATATAATGAGGATGA
AAAATCCCTGAAATTAAAAAACAAAGATCACGAAGTAAAATCAGTTGATA
AATTTGCAAGTGGACTGTTTGAAAATATTCAAAAGGATCTCGGAAAAATT
AAAGATTTAAGTATAAATTATATTCAAGTGAAATATATCAAAAAATCAGA
TTTCCTAAGTTTATTTAACGCGCGATACCTAGAAATGTCGATTCCAATGG
AAATTGATGAAGACAGTTTCATTCCTTTCAATAGCTCTTTCTTTGAAATT
TCCATGAAATGCAACAATGATTCTTCAAACCTTCAATTCAAATTGCAAAT
AGAGAAATGGAGAATATATCTTCATTACTGCAATTATCGCGCTGCTTGCT
CATTGGTGAGTTCCGGTGAGAAATATGAATACAACATCCAATTGAATCAC
GAAGGTAAATACACACCGACAACTGTTACAATAACAAATGAAAACTGCAG
TCAATTGCTCCCAACAAAAATCTATTTCACCACAACCCGCCCGAGTGAAA
TCAGCACAAATTATTCAACACAATCCCGTGAATATTTCAATAATTTAATC
ATTTTTCATTTTTATATATAAATATATCTGTAGTAATGCTCATGATGATA
ATCGGATTTGCAATATATATAAAAAGAAATTTGTAATTAAATTTTGTCAT
GTTTTCAATTTTCATCAATAATATAGCAGTAAAAAGTTTATAAATTATTC
AAAAATATATTTTCATACCAAAA
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protein sequence of SMED30024487-orf-1

>SMED30024487-orf-1 ID=SMED30024487-orf-1|Name=SMED30024487-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=259bp
MIRFRLALMSVIIIIKIIILSIIIPIFTDGSCGDLECYVDRISNTRYVNC
SRGHDPHSKTFICQYNEDEKSLKLKNKDHEVKSVDKFASGLFENIQKDLG
KIKDLSINYIQVKYIKKSDFLSLFNARYLEMSIPMEIDEDSFIPFNSSFF
EISMKCNNDSSNLQFKLQIEKWRIYLHYCNYRAACSLVSSGEKYEYNIQL
NHEGKYTPTTVTITNENCSQLLPTKIYFTTTRPSEISTNYSTQSREYFNN
LIIFHFYI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 7..29