SMED30002867

Overview
NameSMED30002867
Smed IDSMED30002867
Length (bp)1545
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 SMED30002867 (SMED30002867) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002867 (SMED30002867) 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 SMED30002867 (SMED30002867) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002867 (SMED30002867) 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



SMED30002867

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
Category 3 cellSMED30002867 dd_Smed_v6_9764_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002867 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000151:77738..80090 -7343
Homology
[Close]
BLAST of SMED30002867 vs. Planmine SMEST
Match: SMESG000013157.1 (SMESG000013157.1)

HSP 1 Score: 113.62 bits (283), Expect = 3.113e-47
Identity = 56/101 (55.45%), Postives = 73/101 (72.28%), Query Frame = 1 
Query:  952 RQRAEYILARLEK*QRQTNWQVEMARHTLARVNSDIANGRIPSTDGYAPPYGISYELDDPMLEEMSTPMNLVIPRKLFSKEMRDDDRSPREKQDHPYARER 1254
            R +AEY+LARLE+ Q +TN QVE AR  L RVN DIA GRIPSTDGYAP Y +S+ELDDP L+   + M + +PR +  KEMR+++     +++H YARER
Sbjct:  158 RGQAEYLLARLERHQAETNRQVEQARQYLRRVNEDIAAGRIPSTDGYAPQYNVSFELDDPRLQRQMSEMRVAVPRHILPKEMRNENDIAEPQREHSYARER 258

HSP 2 Score: 95.1301 bits (235), Expect = 3.113e-47
Identity = 43/63 (68.25%), Postives = 51/63 (80.95%), Query Frame = 3 
Query:  747 ESWIVASQIIVGFPARSPARCRQAMWDAGFTISPVRESRAGHQEDYDEADLPYVAIKRKPGRT 935
            +SWI AS++I  FPA S ARCRQAMWDAGF+I PVRE+R G Q D +E DL YVAIKR+PGR+
Sbjct:   90 DSWIDASRVIARFPAHSAARCRQAMWDAGFSIFPVRETRGGTQGDSNEVDLSYVAIKREPGRS 152
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BLAST of SMED30002867 vs. Planmine SMEST
Match: SMESG000023390.1 (SMESG000023390.1)

HSP 1 Score: 112.464 bits (280), Expect = 1.860e-46
Identity = 54/100 (54.00%), Postives = 71/100 (71.00%), Query Frame = 1 
Query:  952 RQRAEYILARLEK*QRQTNWQVEMARHTLARVNSDIANGRIPSTDGYAPPYGISYELDDPMLEEMSTPMNLVIPRKLFSKEMRDDDRSPREKQDHPYARE 1251
            R +AE++LARLE+ QRQT  QV  AR  LA +N  IA G IPSTD YAPPY +S+ LDDP L   +  MN+V+PR++ ++EM+D DR   + Q+H YARE
Sbjct:  428 RGQAEFLLARLEEHQRQTKRQVNRARRHLAEINKAIATGDIPSTDRYAPPYNVSFNLDDPNLAGEAEAMNVVVPRRILTREMKDKDRRSNQDQEHSYARE 527

HSP 2 Score: 93.5893 bits (231), Expect = 1.860e-46
Identity = 41/66 (62.12%), Postives = 53/66 (80.30%), Query Frame = 3 
Query:  738 QEDESWIVASQIIVGFPARSPARCRQAMWDAGFTISPVRESRAGHQEDYDEADLPYVAIKRKPGRT 935
            ++D SWI AS++ V FPARS ARCRQ +WDAGF++SPVRESR   + D ++ DLP+VAIKR+PGR 
Sbjct:  357 KDDHSWIDASRVTVRFPARSVARCRQVLWDAGFSVSPVRESRTATRRDDEKVDLPFVAIKREPGRN 422
[Close]
BLAST of SMED30002867 vs. Planmine SMEST
Match: SMESG000026049.1 (SMESG000026049.1)

HSP 1 Score: 137.887 bits (346), Expect = 2.361e-46
Identity = 68/112 (60.71%), Postives = 86/112 (76.79%), Query Frame = 1 
Query:  946 KPRQRAEYILARLEK*QRQTNWQVEMARHTLARVNSDIANGRIPSTDGYAPPYGISYELDDPMLEEMSTPMNLVIPRKLFSKEMRDDDRSPREKQDHPYARERQKR--SPNS 1275
            K +QRAE+ LAR+E  QRQTNWQV MAR  LA++N+DIA GRIP+TD YAP YGIS+ELDDP   E +  M++VIPR+L  K+M+D DRSP E+Q+H YAR R +   +PNS
Sbjct:   47 KTQQRAEFTLARIELHQRQTNWQVVMARRRLAKINADIAAGRIPNTDRYAPAYGISFELDDPAFAEPTMLMDVVIPRRLLPKDMQDSDRSPAERQEHSYARGRSRYRFAPNS 158

HSP 2 Score: 67.781 bits (164), Expect = 2.361e-46
Identity = 32/46 (69.57%), Postives = 36/46 (78.26%), Query Frame = 3 
Query:  819 MWDAGFTISPVRESRAGHQEDYDEADLPYVAIKRKPGRTQPVKAPA 956
            M DAGF+ISP RESR G   DY+EADLPYVAIKR+PGR  P + PA
Sbjct:    1 MLDAGFSISPARESRGGRLNDYEEADLPYVAIKREPGR-NPARNPA 45
[Close]
BLAST of SMED30002867 vs. Planmine SMEST
Match: SMESG000032540.1 (SMESG000032540.1)

HSP 1 Score: 104.76 bits (260), Expect = 3.952e-44
Identity = 54/108 (50.00%), Postives = 70/108 (64.81%), Query Frame = 1 
Query:  952 RQRAEYILARLEK*QRQTNWQVEMARHTLARVNSDIANGRIPSTDGYAPPYGISYELDDPMLEEMSTPMNLVIPRKLFSKEMRDDDRSPREKQDHPYARERQKRSPNS 1275
            R +AEY+LARLE+ +RQT+ +V+ AR  L  +N DIA G IPSTDGYAPPY   + LDDP L   S+ M +V+PR+   +   + +    E  DHPYARER  R  NS
Sbjct:   75 RGQAEYLLARLEEHKRQTDHEVDKARRHLEEINWDIAAGIIPSTDGYAPPYNTPFNLDDPRLNRSSSAMKVVVPRETLIRGWGEANEPANEHHDHPYARERPSRRDNS 182

HSP 2 Score: 93.5893 bits (231), Expect = 3.952e-44
Identity = 41/64 (64.06%), Postives = 51/64 (79.69%), Query Frame = 3 
Query:  744 DESWIVASQIIVGFPARSPARCRQAMWDAGFTISPVRESRAGHQEDYDEADLPYVAIKRKPGRT 935
            + SWI AS++ + FPA S  RCRQAMWDAGF+ISPVRESR G + + D+ DLP+VAIKR+PGR 
Sbjct:    6 ENSWIYASRVTLRFPAHSAVRCRQAMWDAGFSISPVRESRMGSRSNTDDVDLPFVAIKREPGRN 69
[Close]
BLAST of SMED30002867 vs. Planmine SMEST
Match: SMESG000065931.1 (SMESG000065931.1)

HSP 1 Score: 108.612 bits (270), Expect = 4.765e-43
Identity = 51/102 (50.00%), Postives = 73/102 (71.57%), Query Frame = 1 
Query:  952 RQRAEYILARLEK*QRQTNWQVEMARHTLARVNSDIANGRIPSTDGYAPPYGISYELDDPMLEEMSTPMNLVIPRKLFSKEMRDDDRSPREKQDHPYARERQ 1257
            R +AE++L RLE+ Q++T  Q+  AR  LA+VN DIA GRIPSTDGYAP Y +S+ELDDP L      MN+++PR++  +E+R+ + +   +QDH +AR RQ
Sbjct:   81 RGQAEFLLGRLEEHQKETERQIIKARRYLAQVNKDIAEGRIPSTDGYAPSYNVSFELDDPSLCNRLETMNVILPRRVLPRELRNVEENSDSRQDHSFARNRQ 182

HSP 2 Score: 86.2705 bits (212), Expect = 4.765e-43
Identity = 38/62 (61.29%), Postives = 50/62 (80.65%), Query Frame = 3 
Query:  744 DESWIVASQIIVGFPARSPARCRQAMWDAGFTISPVRESRAGHQEDYDEADLPYVAIKRKPG 929
            ++SWI A ++I  FPA + ARCRQAMWDAGF+IS VRE+R G+Q   ++ +LPYVAIKR+PG
Sbjct:   12 EDSWIDAPRVIARFPAHAAARCRQAMWDAGFSISTVRETRFGNQGSSEDVELPYVAIKREPG 73
The following BLAST results are available for this feature:
BLAST of SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 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 SMED30002867 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000013157.13.113e-4755.45SMESG000013157.1[more]
SMESG000023390.11.860e-4654.00SMESG000023390.1[more]
SMESG000026049.12.361e-4660.71SMESG000026049.1[more]
SMESG000032540.13.952e-4450.00SMESG000032540.1[more]
SMESG000065931.14.765e-4350.00SMESG000065931.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002867 ID=SMED30002867|Name=SMED30002867|organism=Schmidtea mediterranea sexual|type=transcript|length=1545bp
TTAGATGATCGTCTATGAGGAAGAACATTGAAAATGAGAATTGATATCAT
TGCGTATTATGATCGTTGAATGTAGTTAACATCAGATCAAGGTTCTTCCA
TCCTTTATATCATACTCGAATATAGAGAATCGCAACATTTGAACATACTT
TGAGGAGTTAGACACACTGACATCATATTGGACGCGATAGCATAGAATCG
TGATGACCCACCGCATAGAGAGAAACTTGACACGTATAAATTACTCATCA
AACGTAAAAATTATTTACCTAAGTTGTTCGAAGAGAATGAGTCGACGACC
TGATCAAAATGAATAAATGACTGAACCAACATAATAATTTTACAAATCGC
TCAAATGGATTTGAAGCGATCACATTAACGTTGAAGAAGATGTGCACGAG
ACACACCCCATACTTAAACAGCCAACGTCAGTGTAGGCCACGTCAGCACA
TTCTAAAAATCAATTTTTTTCTCTCTCTGATCACAAAGCATAAAGCAAAT
CAATTATACCACGTCACTGTGGATAGAAGAAATGTGTTTTCAATCTATAG
TGTGCCGGTCAGTAGATTGATATAAAGAACGAGCACACTAGTTGGAATTT
CATTCTACCGAAAAACCAAACTTATGGAAGCGCCAAGTCAACAAATTTAT
ACCGCCCCATCGAGAAAGGAAGATTGTCGTATCTGCCGACGAGAGGACAG
ATTGAAAGAGAAGCCATCAGAGAAGAGAAACTGCCGCCAAGAAGATGAAT
CCTGGATTGTCGCTTCACAAATCATCGTGGGTTTCCCAGCACGATCCCCT
GCCAGATGCAGACAGGCGATGTGGGACGCGGGATTTACAATTTCCCCCGT
GAGAGAGTCAAGAGCAGGTCATCAGGAGGATTATGACGAGGCCGATCTTC
CTTACGTTGCGATCAAACGGAAGCCGGGCCGAACCCAGCCCGTGAAAGCC
CCGGCAACGCGCCGAATACATTCTGGCTCGTCTTGAGAAATGACAGAGAC
AGACCAATTGGCAGGTGGAAATGGCTAGACACACCCTGGCCAGGGTAAAT
TCTGACATTGCCAACGGAAGGATCCCGAGCACGGACGGATATGCCCCACC
GTACGGCATATCCTATGAACTAGACGATCCAATGTTGGAAGAGATGTCCA
CACCCATGAACTTGGTAATCCCAAGGAAGTTGTTTTCTAAGGAAATGCGA
GACGACGACAGAAGTCCGAGAGAGAAACAAGACCATCCGTACGCTCGAGA
GCGACAGAAACGCAGTCCAAATTCAGACTACCGAAATCCTATGTGGCATT
GAATTGTTATGGAAAATAAATATTGAATTTTACATTTTATTTCTTCACTT
ATAAATTATTTAATCTTTCGATATTAAGACAATAGTAATAGGGAGCTAAA
GCAATCACTATAGTACGGTCAGACAGATATTTAAAAGGTTTTTCCTTTAG
TTGTTGAATATTAGATCTATACAATAACCTAATGTCGACATAGATAAGAA
AATGCTACAGATAAAAATGTGCCATTTACTAACGATTTCTTCTCA
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protein sequence of SMED30002867-orf-1

>SMED30002867-orf-1 ID=SMED30002867-orf-1|Name=SMED30002867-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=121bp
MEAPSQQIYTAPSRKEDCRICRREDRLKEKPSEKRNCRQEDESWIVASQI
IVGFPARSPARCRQAMWDAGFTISPVRESRAGHQEDYDEADLPYVAIKRK
PGRTQPVKAPATRRIHSGSS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell