SMED30027915

Overview
NameSMED30027915
Smed IDSMED30027915
Length (bp)367
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 SMED30027915 (SMED30027915) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027915 (SMED30027915) 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



SMED30027915

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
reproductive organSMED30027915 Contig28235newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
early male germ cellSMED30027915 H_55_10a_-2GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30027915 vs. Planmine SMEST
Match: SMESG000053822.1 (SMESG000053822.1)

HSP 1 Score: 94.7449 bits (234), Expect = 1.177e-23
Identity = 46/73 (63.01%), Postives = 61/73 (83.56%), Query Frame = 2 
Query:   74 TSKVNYKHKLERKQIGERNLRMQLNNQRKTLEENKEQLKELPKLTERLVKTQILIMRFSEARAKEECIMHSPP 292
            T +VNYK +L+RKQ  ERNL+M+++NQ++ ++ENKE+LKELPKLTERL+K Q+LIMRFSE + KEEC  H  P
Sbjct: 5723 TKRVNYKRQLKRKQAKERNLQMKIHNQQRIIKENKERLKELPKLTERLIKAQVLIMRFSENKTKEECEKHPTP 5795
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BLAST of SMED30027915 vs. Planmine SMEST
Match: SMESG000004687.1 (SMESG000004687.1)

HSP 1 Score: 94.3597 bits (233), Expect = 1.841e-23
Identity = 46/73 (63.01%), Postives = 61/73 (83.56%), Query Frame = 2 
Query:   74 TSKVNYKHKLERKQIGERNLRMQLNNQRKTLEENKEQLKELPKLTERLVKTQILIMRFSEARAKEECIMHSPP 292
            T +VNYK +L+RKQ  ERNL+M++ NQ++ ++ENKE+LKELPK+TERL++ QILIMRFSE + KEEC  HS P
Sbjct:  165 TKRVNYKRQLKRKQTKERNLQMKICNQQRIIKENKERLKELPKITERLIRAQILIMRFSENKIKEECERHSTP 237
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BLAST of SMED30027915 vs. Planmine SMEST
Match: SMESG000012882.1 (SMESG000012882.1)

HSP 1 Score: 94.3597 bits (233), Expect = 2.073e-23
Identity = 46/73 (63.01%), Postives = 61/73 (83.56%), Query Frame = 2 
Query:   74 TSKVNYKHKLERKQIGERNLRMQLNNQRKTLEENKEQLKELPKLTERLVKTQILIMRFSEARAKEECIMHSPP 292
            T +VNYK +L+RKQ  ERNL+M+++NQ++ ++E KE+LKELPKLTERL+K Q+LIMRFSE + KEEC  HS P
Sbjct: 3664 TKRVNYKRQLKRKQTKERNLQMKIHNQQRIIKEGKERLKELPKLTERLIKAQVLIMRFSENKIKEECERHSTP 3736
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BLAST of SMED30027915 vs. Planmine SMEST
Match: SMESG000023758.1 (SMESG000023758.1)

HSP 1 Score: 86.6557 bits (213), Expect = 9.065e-21
Identity = 43/66 (65.15%), Postives = 57/66 (86.36%), Query Frame = 2 
Query:   74 TSKVNYKHKLERKQIGERNLRMQLNNQRKTLEENKEQLKELPKLTERLVKTQILIMRFSEARAKEE 271
            T +VNYK +L+RKQ  ERNL+M++ NQ++ ++ENKE+LKELPKLTERL+K Q+LIMRFSE + KEE
Sbjct: 5180 TKRVNYKRQLKRKQTKERNLQMKIYNQQRIIKENKERLKELPKLTERLIKAQVLIMRFSENKTKEE 5245
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BLAST of SMED30027915 vs. Planmine SMEST
Match: SMESG000018175.1 (SMESG000018175.1)

HSP 1 Score: 85.1149 bits (209), Expect = 3.197e-20
Identity = 42/66 (63.64%), Postives = 56/66 (84.85%), Query Frame = 2 
Query:   74 TSKVNYKHKLERKQIGERNLRMQLNNQRKTLEENKEQLKELPKLTERLVKTQILIMRFSEARAKEE 271
            T +VNYK +L+RKQ  ERNL+M++ NQ+  ++ENKE+LKELPK+TERL+K Q+LIMRFSE + KEE
Sbjct:  165 TKRVNYKRQLKRKQTKERNLQMKIYNQQIVIKENKERLKELPKITERLIKAQVLIMRFSENKTKEE 230
The following BLAST results are available for this feature:
BLAST of SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 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 SMED30027915 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000053822.11.177e-2363.01SMESG000053822.1[more]
SMESG000004687.11.841e-2363.01SMESG000004687.1[more]
SMESG000012882.12.073e-2363.01SMESG000012882.1[more]
SMESG000023758.19.065e-2165.15SMESG000023758.1[more]
SMESG000018175.13.197e-2063.64SMESG000018175.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027915 ID=SMED30027915|Name=SMED30027915|organism=Schmidtea mediterranea sexual|type=transcript|length=367bp
ACAAACCCAAGAGGAAATTGAAATATTGAAGGAAGAACTCCAAGAACAAA
AACGAAAAACAAAGAAGCAGAAAACCAGTAAAGTCAACTATAAACATAAA
CTCGAGCGAAAACAAATAGGTGAGAGAAACCTCCGAATGCAACTAAACAA
CCAACGAAAGACACTCGAGGAAAATAAAGAACAATTAAAAGAGCTTCCAA
AACTGACAGAACGATTAGTAAAGACACAAATATTGATAATGAGATTCTCC
GAAGCAAGGGCAAAAGAGGAATGTATAATGCACTCACCACCGGGTGAGCA
GGGAGAATAGCGAGACCTTAAATAAAGCGCAAATCTACTGTATAGAGACA
AAATATGTAAATAATCG
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protein sequence of SMED30027915-orf-1

>SMED30027915-orf-1 ID=SMED30027915-orf-1|Name=SMED30027915-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
QTQEEIEILKEELQEQKRKTKKQKTSKVNYKHKLERKQIGERNLRMQLNN
QRKTLEENKEQLKELPKLTERLVKTQILIMRFSEARAKEECIMHSPPGEQ
GE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002030early male germ cell
PLANA:0002089reproductive organ