SMED30009783

Overview
NameSMED30009783
Smed IDSMED30009783
Length (bp)359
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 SMED30009783 (SMED30009783) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009783 (SMED30009783) 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.
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




SMED30009783

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
X1 cellSMED30009783SMESG000049972.1 SMESG000031902.1 SmedASXL_017518SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
cephalic gangliaSMED30009783SMESG000049972.1 SMESG000031902.1 dd_Smed_v4_13890_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30009783SMESG000049972.1 SMESG000031902.1 dd_Smed_v4_13890_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30009783SMESG000072824.1 SMESG000049972.1 SMESG000031902.1 SMED30031507smed_20140614PMID:26457503
Tu et al., 2015
whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30009783SMESG000072824.1 SMESG000049972.1 SMESG000031902.1 SMED30031507smed_20140614PMID:26457503
Tu et al., 2015
whole organism asexual adult colorimetric in situ hybridization evidence
zeta neoblastSMED30009783SMESG000049972.1 SMESG000031902.1 dd_Smed_v4_13890_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009783 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003465:12032..12558 -1704
v31.047513:1544..2074 +1688
v31.034702:560..1087 -1670
Homology
BLAST of SMED30009783 vs. Planmine SMEST
Match: SMESG000049972.1 (SMESG000049972.1)

HSP 1 Score: 61.6178 bits (148), Expect = 1.938e-12
Identity = 32/48 (66.67%), Postives = 38/48 (79.17%), Query Frame = 3
Query:   99 EYNVNDALDLE-QYLNQIIEINGKHYQINVDDNNEVYLEVLAEDSNDV 239
            E  +N +L  + + L   +EINGKHYQINVDDNNEVYLEVLAEDSND+
Sbjct:   62 ERQLNQSLRTQIRGLEVALEINGKHYQINVDDNNEVYLEVLAEDSNDI 109          

HSP 2 Score: 26.1794 bits (56), Expect = 1.938e-12
Identity = 12/12 (100.00%), Postives = 12/12 (100.00%), Query Frame = 2
Query:  323 IINGNVNIKFNS 358
            IINGNVNIKFNS
Sbjct:  109 IINGNVNIKFNS 120          
BLAST of SMED30009783 vs. Planmine SMEST
Match: SMESG000049972.1 (SMESG000049972.1)

HSP 1 Score: 61.6178 bits (148), Expect = 2.030e-12
Identity = 32/48 (66.67%), Postives = 38/48 (79.17%), Query Frame = 3
Query:   99 EYNVNDALDLE-QYLNQIIEINGKHYQINVDDNNEVYLEVLAEDSNDV 239
            E  +N +L  + + L   +EINGKHYQINVDDNNEVYLEVLAEDSND+
Sbjct:   62 ERQLNQSLRTQIRGLEVALEINGKHYQINVDDNNEVYLEVLAEDSNDI 109          

HSP 2 Score: 26.1794 bits (56), Expect = 2.030e-12
Identity = 12/12 (100.00%), Postives = 12/12 (100.00%), Query Frame = 2
Query:  323 IINGNVNIKFNS 358
            IINGNVNIKFNS
Sbjct:  109 IINGNVNIKFNS 120          
BLAST of SMED30009783 vs. Planmine SMEST
Match: SMESG000049972.1 (SMESG000049972.1)

HSP 1 Score: 61.6178 bits (148), Expect = 2.085e-12
Identity = 32/48 (66.67%), Postives = 38/48 (79.17%), Query Frame = 3
Query:   99 EYNVNDALDLE-QYLNQIIEINGKHYQINVDDNNEVYLEVLAEDSNDV 239
            E  +N +L  + + L   +EINGKHYQINVDDNNEVYLEVLAEDSND+
Sbjct:   62 ERQLNQSLRTQIRGLEVALEINGKHYQINVDDNNEVYLEVLAEDSNDI 109          

HSP 2 Score: 26.1794 bits (56), Expect = 2.085e-12
Identity = 12/12 (100.00%), Postives = 12/12 (100.00%), Query Frame = 2
Query:  323 IINGNVNIKFNS 358
            IINGNVNIKFNS
Sbjct:  109 IINGNVNIKFNS 120          
BLAST of SMED30009783 vs. Planmine SMEST
Match: SMESG000049972.1 (SMESG000049972.1)

HSP 1 Score: 60.8474 bits (146), Expect = 3.843e-12
Identity = 29/44 (65.91%), Postives = 37/44 (84.09%), Query Frame = 3
Query:  108 VNDALDLEQYLNQIIEINGKHYQINVDDNNEVYLEVLAEDSNDV 239
            ++D L ++  +  + +INGKHYQINVDDNNEVYLEVLAEDSND+
Sbjct:    6 LDDDLYIDNLIKALNQINGKHYQINVDDNNEVYLEVLAEDSNDI 49          

HSP 2 Score: 26.1794 bits (56), Expect = 3.843e-12
Identity = 12/12 (100.00%), Postives = 12/12 (100.00%), Query Frame = 2
Query:  323 IINGNVNIKFNS 358
            IINGNVNIKFNS
Sbjct:   49 IINGNVNIKFNS 60          
BLAST of SMED30009783 vs. Planmine SMEST
Match: SMESG000049972.1 (SMESG000049972.1)

HSP 1 Score: 60.4622 bits (145), Expect = 4.069e-12
Identity = 29/44 (65.91%), Postives = 37/44 (84.09%), Query Frame = 3
Query:  108 VNDALDLEQYLNQIIEINGKHYQINVDDNNEVYLEVLAEDSNDV 239
            ++D L ++  +  + +INGKHYQINVDDNNEVYLEVLAEDSND+
Sbjct:    6 LDDDLYIDNLIKALNQINGKHYQINVDDNNEVYLEVLAEDSNDI 49          

HSP 2 Score: 26.1794 bits (56), Expect = 4.069e-12
Identity = 12/12 (100.00%), Postives = 12/12 (100.00%), Query Frame = 2
Query:  323 IINGNVNIKFNS 358
            IINGNVNIKFNS
Sbjct:   49 IINGNVNIKFNS 60          
The following BLAST results are available for this feature:
BLAST of SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 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 SMED30009783 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000049972.11.938e-1266.67SMESG000049972.1[more]
SMESG000049972.12.030e-1266.67SMESG000049972.1[more]
SMESG000049972.12.085e-1266.67SMESG000049972.1[more]
SMESG000049972.13.843e-1265.91SMESG000049972.1[more]
SMESG000049972.14.069e-1265.91SMESG000049972.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009783 ID=SMED30009783|Name=SMED30009783|organism=Schmidtea mediterranea sexual|type=transcript|length=359bp
TTAAATTTAAAGCACGCGATATGTATCAAAATTCACACGAAATCCAAATC
AAAGGTGAAAATTTAGAAAATTTTGAAACTGATTTTCTTGAAACATCAGA
GTATAATGTCAATGACGCATTGGACTTAGAACAATATTTAAATCAAATAA
TTGAAATAAATGGAAAGCATTATCAAATAAATGTCGATGATAACAATGAA
GTGTATTTAGAAGTTTTAGCTGAAGATTCTAACGATGTTGGTAGATGTAA
TTTTATATTTGAAATTGTATATATATATATACATATATCAATACTTATTA
AAAATATTCATGTAACTATTAGATTATAAATGGAAACGTGAATATTAAAT
TTAATTCAG
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protein sequence of SMED30009783-orf-1

>SMED30009783-orf-1 ID=SMED30009783-orf-1|Name=SMED30009783-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
KFKARDMYQNSHEIQIKGENLENFETDFLETSEYNVNDALDLEQYLNQII
EINGKHYQINVDDNNEVYLEVLAEDSNDVGRCNFIFEIVYIYIHISILIK
NIHVTIRL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000026gut
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002142parenchyma