SMED30012095

Overview
NameSMED30012095
Smed IDSMED30012095
Length (bp)1246
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 SMED30012095 (SMED30012095) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012095 (SMED30012095) 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



SMED30012095

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30012095SMESG000030693.1 dd_Smed_v4_15045_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30012095SMESG000030693.1 dd_Smed_v4_15045_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30012095SMESG000030693.1 dd_Smed_v4_15045_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 SMED30012095 vs. Planmine SMEST
Match: SMESG000030693.1 (SMESG000030693.1)

HSP 1 Score: 143.28 bits (360), Expect = 2.282e-39
Identity = 68/74 (91.89%), Postives = 69/74 (93.24%), Query Frame = -1 
Query:  206 IYFYHRPEVEHGFNARMVGSETAGTTDNADRC-----HESGDAAMPPLNTARMMKGRTDGIRGDSDRLSFAAIT 412
            IYFYHRPEVEHGFNARMVGSETAGTTDNADRC     HESGDAAMPPLNTARMM+GRTDGIRGDSDRLSFAAIT
Sbjct:  200 IYFYHRPEVEHGFNARMVGSETAGTTDNADRCRMGHDHESGDAAMPPLNTARMMEGRTDGIRGDSDRLSFAAIT 273
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BLAST of SMED30012095 vs. Planmine SMEST
Match: SMESG000034853.1 (SMESG000034853.1)

HSP 1 Score: 90.1225 bits (222), Expect = 3.212e-21
Identity = 43/60 (71.67%), Postives = 47/60 (78.33%), Query Frame = -1 
Query:  515 MLNKKVFRSIHVNLLSCSEQSRSHVYITAHVADQWRQAWRRANQE*YSDVPPPEGNRRED 694
            MLNKK+ RSIHVNLL CSEQS SHVYI  HVADQWRQAWRR N+E Y D+P     RR+D
Sbjct:    1 MLNKKIIRSIHVNLLFCSEQSGSHVYIPTHVADQWRQAWRRINRERYPDMPRSGERRRDD 60
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BLAST of SMED30012095 vs. Planmine SMEST
Match: SMESG000015578.1 (SMESG000015578.1)

HSP 1 Score: 78.1814 bits (191), Expect = 1.605e-16
Identity = 37/53 (69.81%), Postives = 39/53 (73.58%), Query Frame = -1 
Query:  269 IYFYHRPEVEHGFNARMVGSETAGTTDNADRC-----HESGDAAMPPLNTARM 412
            IYFYHRPEVEHGFNAR  GS TA TTDN DRC     HE G+ A+PPLN  RM
Sbjct:  149 IYFYHRPEVEHGFNARKAGSGTAETTDNMDRCRMRHDHEFGETAVPPLNPTRM 201
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BLAST of SMED30012095 vs. Planmine SMEST
Match: SMESG000000410.1 (SMESG000000410.1)

HSP 1 Score: 58.5362 bits (140), Expect = 8.179e-10
Identity = 29/61 (47.54%), Postives = 40/61 (65.57%), Query Frame = -1 
Query:  455 QSRSHVYITAHVADQWRQAWRRANQE*YSDVPPPEGNRREDPLLAVYEK*PKKFTNDIRPA 637
            +SR  ++++ HVADQWRQAW R  +E Y D+P P  NRR+D LL   E   K+F   I+P+
Sbjct:   45 RSRPFIWVSTHVADQWRQAWARTCKEKYPDMPQPGENRRDDTLLV--EATMKQFRQKIQPS 103
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BLAST of SMED30012095 vs. Planmine SMEST
Match: SMESG000044373.1 (SMESG000044373.1)

HSP 1 Score: 56.225 bits (134), Expect = 2.984e-9
Identity = 27/54 (50.00%), Postives = 35/54 (64.81%), Query Frame = -1 
Query:  506 IHVNLLSCSEQSRSHVYITAHVADQWRQAWRRANQE*YSDVPPPEGNRREDPLL 667
            I  ++   S +S   +Y+  H+ADQWRQAWRR  +E Y DVP P  NRR+D LL
Sbjct:   10 ISNSIAQPSRKSGPFIYVHTHLADQWRQAWRRFGRERYPDVPEPGENRRDDMLL 63
The following BLAST results are available for this feature:
BLAST of SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 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 SMED30012095 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000030693.12.282e-3991.89SMESG000030693.1[more]
SMESG000034853.13.212e-2171.67SMESG000034853.1[more]
SMESG000015578.11.605e-1669.81SMESG000015578.1[more]
SMESG000000410.18.179e-1047.54SMESG000000410.1[more]
SMESG000044373.12.984e-950.00SMESG000044373.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012095 ID=SMED30012095|Name=SMED30012095|organism=Schmidtea mediterranea sexual|type=transcript|length=1246bp
AATCATGGCGGTTTTTATCTCCATATTTGCTAAGTGTGGTAAAGTAACTC
TTTGGGATCTGGGAATTATTATTCTCAGGGTATTCTCCATCCATATATTG
GTTTAATTGGGAATTACAATTTATTTGTTTATGAGTAATCTTGTAATAGG
TTTTTAGTAAGTTGGAGTTTTCAGATCTGGGTATGCCTCTATTTAGAGAA
GTAATTGTTATGGCCGCAAATGACAATCTATCACTATCACCTCTAATTCC
ATCTGTTCTACCTTTCATCATTCTAGCAGTATTCAGAGGGGGCATAGCAG
CATCTCCGGATTCATGGCATCTATCAGCATTATCAGTCGTCCCAGCAGTT
TCAGATCCCACCATTCGGGCATTGAATCCATGTTCCACTTCAGGTCTATG
ATAAAAATAGATGTTATTGTTATTGTAACATCGGTGCAGGCAATTTCCGC
CCAGTGCTGGTCGAATGTCATTTGTAAATTTTTTGGGTTATTTTTCATAA
ACTGCTAGGAGCGGGTCTTCTCGCCGGTTTCCTTCTGGCGGGGGCACGTC
GGAATATCACTCTTGGTTGGCGCGTCGCCACGCTTGTCGCCATTGGTCTG
CGACGTGAGCTGTAATATAAACGTGGGATCTCGATTGTTCTGAACAAGAC
AATAAATTAACATGGATTGATCGAAAGACCTTTTTATTTAACATCCGTCC
ACTTAGATATATTTGAGGGCGTTACTTCTTAGGTCTGAGTCGTGCGAGCG
AATGTCCTATCCCCATAGACGGAAATAATTTTTTATGGGTAATTAGGGTA
GCGTAGGGTCGGCGTTAATTGGTTTCGGGGAGCTAATCGACTGGAAGGGT
GGTAAGAGTAATTAAGATGGCTAACCCCTCCCAAAAATGGTCAGTTTTTC
TTAAGATAGTTCACCTGAGTCGAGATGTCTACTTGTACACACTTTTCCAA
AATTGTGGAACAAATTGAGAATTTCACTACTTGACCTAAATAATTAGAAT
CTTCTAAAATGATTCGAGTAATCCGAGCTTATGCTGGTATAGTTGATTTA
ACTATGATTTCACAAAGGGATTTAAGCCCATCGTCAATCACCTTGAAACA
AATTTTTCTTTTCAAAGCAAAATCAAAAGACAATTTTCAAAAACTGGTCG
GAATAATTTGTTTATTTCAACAAAAGTCGTTCGAAACCCTGTTATTCAGT
TTGCAAAAAATTGGAAAATGGGTTGGAAGGTACCGATACTCGAATT
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protein sequence of SMED30012095-orf-1

>SMED30012095-orf-1 ID=SMED30012095-orf-1|Name=SMED30012095-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=121bp
MVGSETAGTTDNADRCHESGDAAMPPLNTARMMKGRTDGIRGDSDRLSFA
AITITSLNRGIPRSENSNLLKTYYKITHKQINCNSQLNQYMDGEYPENNN
SQIPKSYFTTLSKYGDKNRHD
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell