SMED30014396

Overview
NameSMED30014396
Smed IDSMED30014396
Length (bp)543
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 SMED30014396 (SMED30014396) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014396 (SMED30014396) 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 SMED30014396 (SMED30014396) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014396 (SMED30014396) 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




SMED30014396

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
head regionSMED30014396SMESG000048041.1 SmedASXL_006175SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30014396SMESG000048041.1 dd_Smed_v4_20625_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014396SMESG000048041.1 dd_Smed_v4_20625_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30014396SMESG000048041.1 dd_Smed_v4_20625_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30014396SMESG000048041.1 dd_Smed_v4_20625_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30014396SMESG000048041.1 dd_Smed_v6_20625_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30014396 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.012870:6084..13872 -2316
Homology
BLAST of SMED30014396 vs. TrEMBL
Match: A0A1I8HA02 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 1.525e-10
Identity = 31/88 (35.23%), Postives = 47/88 (53.41%), Query Frame = 3
Query:  234 GGGSNSTILNIRRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDSDQSMIIVWFIFVGFLLGSCVMIIILAELYRSQAVVN 497
             G  ++  L   RFS +AI ML+++++ D HPYGRG   +G           D +  + W +F GF+L +   IIILAE+ R Q  + 
Sbjct:   34 AGFCDTRQLQENRFSAVAIEMLREQEDRDLHPYGRGGRFEGVLYSRRVKVQVDHAKFLAWIVFAGFILLTSGAIIILAEMERRQKTLQ 121          
BLAST of SMED30014396 vs. TrEMBL
Match: A0A4S2LFB0 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_008011 PE=4 SV=1)

HSP 1 Score: 65.4698 bits (158), Expect = 6.349e-10
Identity = 36/96 (37.50%), Postives = 51/96 (53.12%), Query Frame = 3
Query:  195 KNDLKSSLNETEKGGGSNSTILNI---RRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDSDQSMIIVWFIFVGFLLGSCVMIIILAEL 473
            K+ LK SL    +     ST ++    RR S + + ML +++E D HPYGRG   +G       G+  D   ++VWFIF G L+   V II +AEL
Sbjct:   62 KSILKMSLGLGSQVSAPESTAISTETQRRLSSVTLEMLMEREEIDIHPYGRGGIYEGILYTRKEGEPVDMLGLVVWFIFFGSLVMMAVSIIFVAEL 157          
BLAST of SMED30014396 vs. TrEMBL
Match: A0A1I8IHX0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 9.167e-9
Identity = 31/84 (36.90%), Postives = 46/84 (54.76%), Query Frame = 3
Query:  234 GGGSNSTILNIRRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDSDQSMIIVWFIFVGFLLGSCVMIIILAELYRSQ 485
             G  ++  L   RFS +AI ML+++++ D HPYGRG   +G           D +  + W +F GF+L +   IIILAE+ R Q
Sbjct:   34 AGFCDTRQLQENRFSAVAIEMLREQEDRDLHPYGRGGRFEGVLYSRRVKVQVDHAKFLAWIVFAGFILLTSGAIIILAEMERRQ 117          
BLAST of SMED30014396 vs. TrEMBL
Match: A0A2H1BUQ6 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_14327 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 3.212e-7
Identity = 33/95 (34.74%), Postives = 51/95 (53.68%), Query Frame = 3
Query:  195 KNDLKSSLNETEKGGGSNSTILNI--RRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDSDQSMIIVWFIFVGFLLGSCVMIIILAEL 473
            K+ LKSSL      G S+  +  +  RR S I + ML +++E D HPYGRG   +G        ++ D  +I+VW IF   +L   + ++ +AEL
Sbjct:   69 KSILKSSLGLDTMTGISDIPLSTVDQRRVSSITLEMLMEREEIDVHPYGRGGIYEGILYSHKKEEELDFVVILVWLIFSSSVLMISIAVVFVAEL 163          
BLAST of SMED30014396 vs. TrEMBL
Match: A0A4E0QVR4 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_009859 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 4.487e-7
Identity = 33/95 (34.74%), Postives = 51/95 (53.68%), Query Frame = 3
Query:  195 KNDLKSSLNETEKGGGSNSTILNI--RRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDSDQSMIIVWFIFVGFLLGSCVMIIILAEL 473
            K+ LKSSL      G S+  +  +  RR S I + ML +++E D HPYGRG   +G        ++ D  +I+VW IF   +L   + ++ +AEL
Sbjct:   66 KSILKSSLGLDTMTGISDIPLSTVDQRRVSSITLEMLMEREEIDVHPYGRGGIYEGILYSHKKEEELDFVVILVWLIFSSSVLMISIAVVFVAEL 160          
BLAST of SMED30014396 vs. Planmine SMEST
Match: SMESG000048041.1 (SMESG000048041.1)

HSP 1 Score: 276.559 bits (706), Expect = 9.321e-97
Identity = 135/135 (100.00%), Postives = 135/135 (100.00%), Query Frame = 3
Query:  111 MPDDKQVKLVGKSPKTVSFTNLGYENDDKNDLKSSLNETEKGGGSNSTILNIRRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDSDQSMIIVWFIFVGFLLGSCVMIIILAELYRSQAVVNISYSNG 515
            MPDDKQVKLVGKSPKTVSFTNLGYENDDKNDLKSSLNETEKGGGSNSTILNIRRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDSDQSMIIVWFIFVGFLLGSCVMIIILAELYRSQAVVNISYSNG
Sbjct:    1 MPDDKQVKLVGKSPKTVSFTNLGYENDDKNDLKSSLNETEKGGGSNSTILNIRRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDSDQSMIIVWFIFVGFLLGSCVMIIILAELYRSQAVVNISYSNG 135          
BLAST of SMED30014396 vs. Planmine SMEST
Match: SMESG000081746.1 (SMESG000081746.1)

HSP 1 Score: 62.7734 bits (151), Expect = 6.417e-13
Identity = 31/75 (41.33%), Postives = 42/75 (56.00%), Query Frame = 3
Query:  267 RRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSGKDS-DQSMIIVWFIFVGFLLGSCVMIIILAELYRSQA 488
             RFS +A+ +L+  D  D HP+GRG    G    +   K+  D S I VW +F+GF L    +IIILAE+ R Q 
Sbjct:   41 HRFSSVALDLLRVNDNEDIHPFGRGGKFTGVLYGNQKIKNRIDHSKIFVWILFIGFALTGSALIIILAEIDRKQT 115          
The following BLAST results are available for this feature:
BLAST of SMED30014396 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 SMED30014396 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 SMED30014396 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 SMED30014396 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 SMED30014396 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 SMED30014396 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 SMED30014396 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 SMED30014396 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8HA021.525e-1035.23Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A4S2LFB06.349e-1037.50Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A1I8IHX09.167e-936.90Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A2H1BUQ63.212e-734.74Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A4E0QVR44.487e-734.74Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
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BLAST of SMED30014396 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 SMED30014396 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 SMED30014396 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 SMED30014396 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 SMED30014396 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 SMED30014396 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000048041.19.321e-97100.00SMESG000048041.1[more]
SMESG000081746.16.417e-1341.33SMESG000081746.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014396 ID=SMED30014396|Name=SMED30014396|organism=Schmidtea mediterranea sexual|type=transcript|length=543bp
AATGAGAACATATTATCAACGAATTATAATTATCTATATTCTGATTGGTG
GAAAATTTATTCAGTATTTTCTTTGATTAAATGGATATTCTCATTAATGA
GAGTAATAAAATGCCTGATGACAAACAAGTAAAGCTTGTCGGAAAATCTC
CAAAAACCGTTTCATTCACAAATTTGGGATATGAAAATGATGACAAAAAC
GATTTGAAGTCTTCACTGAATGAAACTGAGAAAGGGGGAGGCTCAAATTC
GACAATACTAAATATTCGAAGGTTTTCCGATATTGCCATCACTATGCTGA
AAGATAAAGACGAGACTGATGAACATCCTTACGGGCGAGGGAAAACAGTA
GACGGATGTTTTAATCGCTCATCATCGGGAAAGGATTCCGACCAAAGTAT
GATAATCGTTTGGTTCATATTTGTTGGATTTCTTTTGGGCTCCTGCGTTA
TGATAATCATTCTAGCAGAATTATACAGGAGCCAGGCGGTGGTAAACATA
AGCTACTCAAACGGATGACCGGGCATTTGAACCAGATATTGCA
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protein sequence of SMED30014396-orf-1

>SMED30014396-orf-1 ID=SMED30014396-orf-1|Name=SMED30014396-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=146bp
MDILINESNKMPDDKQVKLVGKSPKTVSFTNLGYENDDKNDLKSSLNETE
KGGGSNSTILNIRRFSDIAITMLKDKDETDEHPYGRGKTVDGCFNRSSSG
KDSDQSMIIVWFIFVGFLLGSCVMIIILAELYRSQAVVNISYSNG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 107..129