SMED30029515

Overview
NameSMED30029515
Smed IDSMED30029515
Length (bp)434
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 SMED30029515 (SMED30029515) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029515 (SMED30029515) 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




SMED30029515

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30029515SMESG000019002.1 dd_Smed_v4_19312_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30029515 vs. TrEMBL
Match: A0A151IP03 (Zinc finger MYM-type protein 1 OS=Cyphomyrmex costatus OX=456900 GN=ALC62_01831 PE=4 SV=1)

HSP 1 Score: 51.9878 bits (123), Expect = 6.298e-6
Identity = 25/37 (67.57%), Postives = 32/37 (86.49%), Query Frame = 3
Query:  309 DFLSIFPNLSISLKILFTIPVSGSSRENSFSKLKIIK 419
            D ++IFPNLSISL+IL T+PV+ ++ E SFSKLKIIK
Sbjct:   14 DLINIFPNLSISLRILLTMPVTVATGERSFSKLKIIK 50          
BLAST of SMED30029515 vs. Planmine SMEST
Match: SMESG000026726.1 (SMESG000026726.1)

HSP 1 Score: 45.0542 bits (105), Expect = 2.556e-6
Identity = 23/41 (56.10%), Postives = 32/41 (78.05%), Query Frame = 3
Query:  297 IICIDFLSIFPNLSISLKILFTIPVSGSSRENSFSKLKIIK 419
            I+  + + I+PNL I+LKIL T+PVS +S E SFS+LK+IK
Sbjct:  103 ILQNELIPIYPNLYIALKILLTMPVSVASGERSFSRLKLIK 143          
BLAST of SMED30029515 vs. Planmine SMEST
Match: SMESG000000228.1 (SMESG000000228.1)

HSP 1 Score: 45.4394 bits (106), Expect = 3.401e-6
Identity = 21/32 (65.62%), Postives = 27/32 (84.38%), Query Frame = 3
Query:  324 FPNLSISLKILFTIPVSGSSRENSFSKLKIIK 419
            FPN++ SLK+L T+PVS +S + SFSKLKIIK
Sbjct:  183 FPNVATSLKLLLTVPVSVASGKRSFSKLKIIK 214          
BLAST of SMED30029515 vs. Planmine SMEST
Match: SMESG000000228.1 (SMESG000000228.1)

HSP 1 Score: 45.4394 bits (106), Expect = 3.402e-6
Identity = 21/32 (65.62%), Postives = 27/32 (84.38%), Query Frame = 3
Query:  324 FPNLSISLKILFTIPVSGSSRENSFSKLKIIK 419
            FPN++ SLK+L T+PVS +S + SFSKLKIIK
Sbjct:  184 FPNVATSLKLLLTVPVSVASGKRSFSKLKIIK 215          
BLAST of SMED30029515 vs. Planmine SMEST
Match: SMESG000000228.1 (SMESG000000228.1)

HSP 1 Score: 45.4394 bits (106), Expect = 3.938e-6
Identity = 21/32 (65.62%), Postives = 27/32 (84.38%), Query Frame = 3
Query:  324 FPNLSISLKILFTIPVSGSSRENSFSKLKIIK 419
            FPN++ SLK+L T+PVS +S + SFSKLKIIK
Sbjct:  184 FPNVATSLKLLLTVPVSVASGKRSFSKLKIIK 215          
BLAST of SMED30029515 vs. Planmine SMEST
Match: SMESG000036749.1 (SMESG000036749.1)

HSP 1 Score: 45.0542 bits (105), Expect = 5.092e-6
Identity = 22/32 (68.75%), Postives = 27/32 (84.38%), Query Frame = 3
Query:  324 FPNLSISLKILFTIPVSGSSRENSFSKLKIIK 419
            FPN++ SLK+L T+PVS +S E SFSKLKIIK
Sbjct:  691 FPNVATSLKLLLTVPVSVASGERSFSKLKIIK 722          
The following BLAST results are available for this feature:
BLAST of SMED30029515 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 SMED30029515 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 SMED30029515 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 SMED30029515 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 SMED30029515 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 SMED30029515 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 SMED30029515 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 SMED30029515 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A151IP036.298e-667.57Zinc finger MYM-type protein 1 OS=Cyphomyrmex cost... [more]
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BLAST of SMED30029515 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 SMED30029515 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 SMED30029515 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 SMED30029515 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 SMED30029515 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 SMED30029515 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000026726.12.556e-656.10SMESG000026726.1[more]
SMESG000000228.13.401e-665.63SMESG000000228.1[more]
SMESG000000228.13.402e-665.63SMESG000000228.1[more]
SMESG000000228.13.938e-665.63SMESG000000228.1[more]
SMESG000036749.15.092e-668.75SMESG000036749.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029515 ID=SMED30029515|Name=SMED30029515|organism=Schmidtea mediterranea sexual|type=transcript|length=434bp
AGAAACGCCACCGTATATATATTTAAAAAATGATTTATTTATTATATTCA
CGGACGCTCCAATTCTACTGGCGTCCCTGTGCTAAGTACATTTAGCACAA
TGAATAATGAAAAAAAAAGAGATATTGACTAACTGTTTTCAAGTTCAAAA
AATACTGACAACCAAATTAAAAGGCTGCACGTTGACTTTCTTTATAATCT
AGGAAATATCAACATCGACATTATCTTTGAAAATTGTGAAAATTTATATA
TTGTGTCGACAGATGAAAAAAGAAATTAATTAAATATAGATGGATTATAA
TTTGTATCGATTTTCTATCGATTTTTCCAAATTTATCTATATCTCTAAAA
ATCTTATTTACTATTCCAGTAAGTGGATCATCAAGAGAGAATTCATTTTC
TAAGCTTAAAATTATAAAAATTATTCACGCTGCT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR008906HATC_C_dom
Vocabulary: molecular function
TermDefinition
GO:0046983protein dimerization activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR008906HAT, C-terminal dimerisation domainPFAMPF05699Dimer_Tnp_hATcoord: 9..37
e-value: 1.2E-5
score: 24.9