SMED30017590

Overview
NameSMED30017590
Smed IDSMED30017590
Length (bp)902
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 SMED30017590 (SMED30017590) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017590 (SMED30017590) 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 SMED30017590 (SMED30017590) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017590 (SMED30017590) 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.
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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



SMED30017590

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30017590h1SMcG0002345 SmedASXL_080058SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30017590h1SMcG0002362 Contig4030GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017590h1SMcG0002345 Contig4030GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30017590h1SMcG0002345 dd_Smed_v4_3944_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017590h1SMcG0002345 dd_Smed_v4_3944_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30017590h1SMcG0002345 dd_Smed_v4_3944_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30017590h1SMcG0002345 dd_Smed_v4_3944_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30017590h1SMcG0002345 dd_Smed_v4_3944_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30017590h1SMcG0002345 dd_Smed_v6_3944_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30017590h1SMcG0002345 OX_Smed_1.0.07821ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017590 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.020393:1516..2396 -3422
Homology
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BLAST of SMED30017590 vs. Ensembl Fly
Match: CG30419 (gene:FBgn0050419 transcript:FBtr0072275)

HSP 1 Score: 78.9518 bits (193), Expect = 1.376e-16
Identity = 51/196 (26.02%), Postives = 87/196 (44.39%), Query Frame = 3 
Query:  246 QLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPWYRRKRCHITQMIG--------------------------------------------------GVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDREMTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRK 683
            Q  Y+ESRG+ C++L++ +G   K+ L+  EGWA+ A  SY  +   +++  RC I +  G                                                      P++    I++G  GC       +KS   + D     F+L LTS +S ED+ +GYCLTGF++   +V + ++MTH+A+++R+
Sbjct:  102 QEIYFESRGKSCKKLLKFNGNSNKILLYPEEGWARTASSSYWTITPCFWQPNRCRIVECSGTQRRATKARMLPLEQQGSLLIAGHFRRTTAGGGGAASPAGGGASGNGSVAATPTPAIPADAIRTGSTGC-------DKSQPAWND----EFKLYLTSNISMEDYNMGYCLTGFVERRCQVTNTFQMTHFAVIKRQ 286
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BLAST of SMED30017590 vs. TrEMBL
Match: A0A210PTT2 (Uncharacterized protein OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT06156 PE=4 SV=1)

HSP 1 Score: 135.961 bits (341), Expect = 4.397e-36
Identity = 69/150 (46.00%), Postives = 96/150 (64.00%), Query Frame = 3 
Query:  240 MVQLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPWYRRKRCHITQMIGGVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDREMTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRKGY 689
            MVQLFYYE+RG+ C+++  ++G P KV L  YEGWAQPAL SY LL+  W+ R RC I + + GVK+ +  G+    G  G M I G       K++D     F+++LT+ +S  DF LGYC+TG L+ G K     ++TH+AMV+RKGY
Sbjct:    1 MVQLFYYETRGKCCRKVFNYEGYPTKVMLFPYEGWAQPALVSYWLLKTYWWSRSRCKIVE-VSGVKKRTTKGKMADKG-SGAMTITG-------KFKDTVSPDFKMTLTTNISNADFQLGYCVTGTLERGDKKRSDLQLTHFAMVKRKGY 141
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BLAST of SMED30017590 vs. TrEMBL
Match: V4B1X5 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_111605 PE=4 SV=1)

HSP 1 Score: 129.798 bits (325), Expect = 9.871e-34
Identity = 65/150 (43.33%), Postives = 96/150 (64.00%), Query Frame = 3 
Query:  240 MVQLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPWYRRKRCHITQMIGGVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDREMTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRKGY 689
            MVQLFYYE+RG+ C+++  ++G P KV +  YEGWAQPAL +Y LL+  W+ R +C I + + G K+ S  G+ I  G +G MII GR       ++D     F++ LT+ +   DF +GYC+TG L+ G K     ++THY+M++RKGY
Sbjct:    1 MVQLFYYETRGKCCRKVFSYEGCPTKVLMFPYEGWAQPALITYWLLKTYWWSRSKCKIVE-VTGPKKTSTKGKMIDKG-NGTMIITGR-------FKDSSSPDFRMFLTTNIDPGDFQMGYCVTGTLERGDKRKSDLQLTHYSMIKRKGY 141
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BLAST of SMED30017590 vs. TrEMBL
Match: R7TFG4 (Uncharacterized protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_212589 PE=4 SV=1)

HSP 1 Score: 122.479 bits (306), Expect = 7.973e-31
Identity = 58/150 (38.67%), Postives = 87/150 (58.00%), Query Frame = 3 
Query:  240 MVQLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPWYRRKRCHITQMIGGVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDREMTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRKGY 689
            MVQ+FYY+ RG+ C +++RH+G P K+ L  YEGWA PA  S+  ++ PW+ R RC I +     K+       +     G M++ GR    +   +      F+L LT+ VS  DF LGY +TG L+ G + +   +MTH+AM++RKGY
Sbjct:    1 MVQMFYYDCRGKNCHKVLRHEGFPSKILLFPYEGWAAPATTSFFNIKLPWWSRSRCEIAESCTAGKKSRTRNAKVVECRGGTMVVVGRFKGVAHNPD------FKLVLTTNVSNADFQLGYSITGTLERGDRKEGKMQMTHFAMIKRKGY 144
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BLAST of SMED30017590 vs. TrEMBL
Match: K1PCZ5 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10003466 PE=4 SV=1)

HSP 1 Score: 120.939 bits (302), Expect = 2.741e-30
Identity = 60/150 (40.00%), Postives = 91/150 (60.67%), Query Frame = 3 
Query:  240 MVQLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPWYRRKRCHITQMIGGVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDREMTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRKGY 689
            MVQLFYYE+RG+ C+++  ++G P +V L  YEGWA P   +Y  L+  W+ R RC I + + G K+ S  G+    G  G M+I G       K+++     F+++LT+ +S EDF LGYC+TG L+ G K     ++  +AMV+R+GY
Sbjct:    1 MVQLFYYENRGKCCRKVFNYEGYPTRVMLFPYEGWAHPVPVTYWTLKTYWWNRSRCKIVE-VSGTKRRSTKGKMADKG-SGAMVISG-------KFKNTPSPDFRMTLTTNISNEDFQLGYCVTGTLERGDKKKGDLQLAQFAMVKRRGY 141
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BLAST of SMED30017590 vs. TrEMBL
Match: A0A0R3X2V4 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS7629 PE=4 SV=1)

HSP 1 Score: 117.857 bits (294), Expect = 5.770e-29
Identity = 59/150 (39.33%), Postives = 90/150 (60.00%), Query Frame = 3 
Query:  240 MVQLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPWYRRKRCHITQMIGGVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDREMTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRKGY 689
            MVQLFYYE+ G+RC +LIR +G  + ++L+A+EG    ++C+   LRFPW+  + C + +  G  K+     + + +  DG + + G+     +    +   HF + LTS V++ DF  GY LTG LQ G +  + WE TH+AMVRRKGY
Sbjct:    1 MVQLFYYETLGRRCDKLIRINGRQMSLELYAFEGIPSTSMCNRWELRFPWFTCRYCSVVKTCGPNKRYVARAKAMCTKHDGALFVTGKFKDDEEGMAGKP--HFCIFLTSNVTQSDFHAGYILTGTLQRGDRRKNDWETTHFAMVRRKGY 148
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BLAST of SMED30017590 vs. Planmine SMEST
Match: SMESG000037675.1 (SMESG000037675.1)

HSP 1 Score: 315.464 bits (807), Expect = 5.367e-110
Identity = 150/150 (100.00%), Postives = 150/150 (100.00%), Query Frame = 3 
Query:  240 MVQLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPWYRRKRCHITQMIGGVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDREMTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRKGY 689
            MVQLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPWYRRKRCHITQMIGGVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDREMTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRKGY
Sbjct:    1 MVQLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPWYRRKRCHITQMIGGVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDREMTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRKGY 150
The following BLAST results are available for this feature:
BLAST of SMED30017590 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 SMED30017590 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 SMED30017590 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG304191.376e-1626.02gene:FBgn0050419 transcript:FBtr0072275[more]
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BLAST of SMED30017590 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 SMED30017590 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 SMED30017590 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 SMED30017590 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 SMED30017590 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A210PTT24.397e-3646.00Uncharacterized protein OS=Mizuhopecten yessoensis... [more]
V4B1X59.871e-3443.33Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
R7TFG47.973e-3138.67Uncharacterized protein OS=Capitella teleta OX=283... [more]
K1PCZ52.741e-3040.00Uncharacterized protein OS=Crassostrea gigas OX=29... [more]
A0A0R3X2V45.770e-2939.33Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
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BLAST of SMED30017590 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 SMED30017590 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 SMED30017590 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 SMED30017590 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 SMED30017590 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 SMED30017590 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000037675.15.367e-110100.00SMESG000037675.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017590 ID=SMED30017590|Name=SMED30017590|organism=Schmidtea mediterranea sexual|type=transcript|length=902bp
TAGCATTAATAATCCACTGCATGCAATTGCTGTGTGGTTTTTTTTTTATT
ATTTAGATGCAGTAAAAGCATACAGACTCAATTCGTTATTTTTCTGTTCA
GTGAAAAACTACTGATTAATTGTAAGCAAATGAGTATATATTCGTTATCT
TAGGCAATTATTTTTATTATTGTCATTTATCACAAAATCCCATAACAAAC
AATTTGAAAGGATACAATTGAAATTATACGCGATCAGTAATGGTCCAACT
GTTCTATTATGAGAGCAGAGGCCAAAGATGTCAAGAGTTAATTCGCCATG
ATGGTCCACCAATCAAAGTTCAACTGCATGCTTATGAAGGCTGGGCTCAA
CCGGCCTTATGTTCATATTTATTGCTCAGATTCCCGTGGTATCGAAGAAA
ACGTTGTCATATCACCCAAATGATTGGAGGTGTCAAACAACCGTCATTGA
CTGGCCGTTTTATCCAATCCGGAGTAGATGGCTGTATGATAATTAGAGGC
AGACTTAACAAAAGTTCCAAAAAGTACGAAGACCGCGAAATGACCCATTT
TCAATTAAGTTTAACGTCAGCGGTTAGCGAAGAAGACTTTGTCCTCGGAT
ATTGTTTGACTGGGTTTTTGCAGCATGGACGCAAAGTAGACGATTGGTGG
GAGATGACACATTATGCCATGGTTCGTCGCAAAGGATATTAATGCCATGT
TTTTACGTTGATTTTCGGTTTCGTTGCACACTATCAATAATTATCCAAAC
ATGTTATTTTGTTTGTATTGGTAACATTTCAGTACAATTCACAGCAGTTG
ACTTCTTTTTTTCGTTTCATTTCTATAATTTCTGTTTATTTCTGAAAGTC
CAAGCATTTCGATAATGTATTGTGATAAATTGGTCAAATATAAATTTATT
GG
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protein sequence of SMED30017590-orf-1

>SMED30017590-orf-1 ID=SMED30017590-orf-1|Name=SMED30017590-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=151bp
MVQLFYYESRGQRCQELIRHDGPPIKVQLHAYEGWAQPALCSYLLLRFPW
YRRKRCHITQMIGGVKQPSLTGRFIQSGVDGCMIIRGRLNKSSKKYEDRE
MTHFQLSLTSAVSEEDFVLGYCLTGFLQHGRKVDDWWEMTHYAMVRRKGY
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head