SMED30022007

Overview
NameSMED30022007
Smed IDSMED30022007
Length (bp)422
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30022007 (SMED30022007) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022007 (SMED30022007) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30022007

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30022007 dd_Smed_v4_90717_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30022007 dd_Smed_v4_90717_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30022007 dd_Smed_v4_90717_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30022007 dd_Smed_v4_90717_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30022007 dd_Smed_v4_90717_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022007 dd_Smed_v4_90717_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30022007 dd_Smed_v4_90717_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30022007 dd_Smed_v4_90717_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
Homology
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BLAST of SMED30022007 vs. Planmine SMEST
Match: SMESG000015457.1 (SMESG000015457.1)

HSP 1 Score: 110.923 bits (276), Expect = 8.222e-32
Identity = 56/121 (46.28%), Postives = 76/121 (62.81%), Query Frame = 1 
Query:   64 PITTQENTIFYKSQVELKMLATPMGIDPHQTVLCYIMYAFLNGTTKITMKEAAICWRKIKSMTKFDPEFTLLMERLMTEPSEK----TEILVALKTFESLITDVVNYDKLPNYKYLNFFCN 414
            P  T+++ IF  S  EL +LA   G DPH+  LCY M+ FLNG+ +I + +A   WR+I  + K D +F+ LME L+T+P E     + I  AL+ F  LI D VNYD+L N+KYLNFF N
Sbjct:   27 PKVTEKDAIFLNSLSELCLLALKKGADPHEIELCYKMFVFLNGSAEIQISDAIGYWREINFIAKIDSDFSDLMELLLTKPLESRDLPSRIKYALEIFRKLIADAVNYDELLNHKYLNFFTN 147
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BLAST of SMED30022007 vs. Planmine SMEST
Match: SMESG000012629.1 (SMESG000012629.1)

HSP 1 Score: 89.3521 bits (220), Expect = 5.351e-23
Identity = 49/120 (40.83%), Postives = 68/120 (56.67%), Query Frame = 1 
Query:   67 ITTQENTIFYKSQVELKMLATPMGIDPHQTVLCYIMYAFLNGTTKITMKEAAICWRKIKSMTKFDPEFTLLMERLMTEPSE----KTEILVALKTFESLITDVVNYDKLPNYKYLNFFCN 414
            I    N IF  S  EL+++      DP+   LCY +Y FLNG+ +I + +A   W KIK         +  +++L+T+P E    +++IL AL  F  LI DVV +D L NYKYLNFFCN
Sbjct:   54 IDNYGNKIFENSLSELRLITIENNADPYLIELCYKIYVFLNGSMEIPIDDAVKFWNKIKLTDILGSYASQQIDQLLTKPLELEGLQSKILYALNIFRDLIADVVTFDILLNYKYLNFFCN 173
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BLAST of SMED30022007 vs. Planmine SMEST
Match: SMESG000047318.1 (SMESG000047318.1)

HSP 1 Score: 88.1965 bits (217), Expect = 3.360e-22
Identity = 52/114 (45.61%), Postives = 72/114 (63.16%), Query Frame = 1 
Query:   82 NTIFYKSQVELKMLATPMGIDPHQTVLCYIMYAFLNGTTKITMKEAAICWRKIKSMTKFDPEFTLLMERLMTEPSEKTEIL-----VALKTFESLITDVVNYDKLPNYKYLNFF 408
            + IF KS  EL++L+    IDPH   LCY ++ FLNG+ +I +  A   W++I S   FDP+F+  ME+++T+P  KTE L      ALKT + LI D VN DKL N+K+L FF
Sbjct:   98 DPIFEKSLHELRLLSK-GNIDPHLLELCYKIHVFLNGSKEIPLNIAIGHWKEINSTGIFDPDFSEHMEQILTKPF-KTEGLQLKIEYALKTSDKLIADAVNPDKLLNHKHLKFF 209
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BLAST of SMED30022007 vs. Planmine SMEST
Match: SMESG000030578.1 (SMESG000030578.1)

HSP 1 Score: 85.5001 bits (210), Expect = 3.475e-20
Identity = 54/126 (42.86%), Postives = 74/126 (58.73%), Query Frame = 1 
Query:    1 TSILANTKANTYFYETYSINQPITTQENTIFYKSQVELKMLATPMGIDPHQTVLCYIMYAFLNGTTKITMKEAAICWRKIKSMTKFDPEFTLLMERLMTEPSE----KTEILVALKTFESLITDVV 366
            TSILANT  NT F ET++I  P     +TIF  S  EL++LA     DPH   L Y M+ FLNGTT++T+ +A   W +I +   FD   T  M+ L+T+P      +++I  ALKTF+  ITD +
Sbjct:   29 TSILANTNMNTCFDETHNILPPT----DTIFESSLSELRILADENNYDPHIIELNYRMFVFLNGTTEVTITDATRYWNEICNTCTFDINITETMQLLLTKPLHYEDFQSKINYALKTFQDAITDAI 150
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BLAST of SMED30022007 vs. Planmine SMEST
Match: SMESG000062768.1 (SMESG000062768.1)

HSP 1 Score: 81.2629 bits (199), Expect = 1.183e-19
Identity = 45/109 (41.28%), Postives = 69/109 (63.30%), Query Frame = 1 
Query:   82 NTIFYKSQVELKMLATPMGIDPHQTVLCYIMYAFLNGTTKITMKEAAICWRKIKSMTKFDPEFTLLMERLMTEPSE----KTEILVALKTFESLITDVVNYDKLPNYKY 396
            + IF KS   L++L+    IDPH   LCY ++ FLNG+ +I++  A   W++I S   FDP+F+  ME+++T+P +    + +I  ALKTF+ LI D VN DKL  +K+
Sbjct:  107 DPIFEKSLHALRLLSK-RNIDPHLLELCYKIHVFLNGSKEISLNIAIGHWKEINSTGIFDPDFSEHMEQILTKPFKTEDLQLKIEYALKTFDKLIADAVNPDKLLIHKH 214
The following BLAST results are available for this feature:
BLAST of SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 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 SMED30022007 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000015457.18.222e-3246.28SMESG000015457.1[more]
SMESG000012629.15.351e-2340.83SMESG000012629.1[more]
SMESG000047318.13.360e-2245.61SMESG000047318.1[more]
SMESG000030578.13.475e-2042.86SMESG000030578.1[more]
SMESG000062768.11.183e-1941.28SMESG000062768.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022007 ID=SMED30022007|Name=SMED30022007|organism=Schmidtea mediterranea sexual|type=transcript|length=422bp
ACATCTATTTTAGCCAATACCAAAGCGAATACCTATTTTTATGAAACTTA
CAGTATTAACCAACCCATAACTACTCAAGAAAATACAATATTCTACAAAA
GCCAAGTAGAACTAAAAATGCTAGCTACACCAATGGGTATTGACCCACAT
CAAACTGTACTTTGCTACATAATGTACGCATTTCTAAATGGAACAACCAA
AATAACCATGAAAGAGGCTGCCATATGTTGGAGAAAGATCAAATCTATGA
CCAAGTTTGATCCAGAATTTACTCTCCTGATGGAACGTTTAATGACAGAG
CCGTCTGAGAAAACAGAAATACTCGTTGCCCTAAAAACTTTTGAAAGTTT
AATCACGGATGTGGTAAATTATGACAAATTGCCAAATTATAAATACCTTA
ATTTCTTTTGTAACCATAACTA
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protein sequence of SMED30022007-orf-1

>SMED30022007-orf-1 ID=SMED30022007-orf-1|Name=SMED30022007-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=140bp
TSILANTKANTYFYETYSINQPITTQENTIFYKSQVELKMLATPMGIDPH
QTVLCYIMYAFLNGTTKITMKEAAICWRKIKSMTKFDPEFTLLMERLMTE
PSEKTEILVALKTFESLITDVVNYDKLPNYKYLNFFCNHN
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell