SMED30033873

Overview
NameSMED30033873
Smed IDSMED30033873
Length (bp)454
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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 SMED30033873 (SMED30033873) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033873 (SMED30033873) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30033873 (SMED30033873) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033873 (SMED30033873) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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



SMED30033873

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30033873SMESG000003398.1 Contig124GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
nervous systemSMED30033873SMESG000003398.1 dd_Smed_v4_248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30033873SMESG000003398.1 dd_Smed_v4_248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30033873SMESG000003398.1 dd_Smed_v4_248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30033873SMESG000003398.1 dd_Smed_v4_248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30033873SMESG000003398.1 dd_Smed_v4_248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30033873SMESG000003398.1 dd_Smed_v4_248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30033873SMESG000003398.1 dd_Smed_v6_248_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30033873SMESG000003398.1 dd_Smed_v4_248_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
SMED30033873 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006140:11176..11623 -1773
Homology
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BLAST of SMED30033873 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000006261.1 (pep scaffold:Pmarinus_7.0:GL477433:28222:29567:1 gene:ENSPMAG00000005664.1 transcript:ENSPMAT00000006261.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 44.2838 bits (103), Expect = 1.073e-6
Identity = 27/74 (36.49%), Postives = 40/74 (54.05%), Query Frame = -3 
Query:  117 VIVK-FGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG 335
            V VK   ++    EV    SV  LK+++ QK GIA     L + +  L DD+ L+ Y IQ +S + M  +L+GG
Sbjct:   78 VFVKTLANKTLTIEVKLSNSVLSLKQKVHQKAGIAVNQQILTFGSHTLEDDQKLESYGIQQHSTITMQGRLRGG 151
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BLAST of SMED30033873 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000006254.1 (pep scaffold:Pmarinus_7.0:GL477433:3744:20801:-1 gene:ENSPMAG00000005642.1 transcript:ENSPMAT00000006254.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 44.669 bits (104), Expect = 2.357e-6
Identity = 27/74 (36.49%), Postives = 40/74 (54.05%), Query Frame = -3 
Query:  117 VIVK-FGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG 335
            V VK   ++    EV    SV  LK+++ QK GIA     L + +  L DD+ L+ Y IQ +S + M  +L+GG
Sbjct:  154 VFVKTLANKTLTIEVKLSNSVLSLKQKVHQKAGIAVNQQILTFGSHTLEDDQKLESYGIQQHSTITMQGRLRGG 227

HSP 2 Score: 44.669 bits (104), Expect = 2.357e-6
Identity = 27/74 (36.49%), Postives = 40/74 (54.05%), Query Frame = -3 
Query:  117 VIVK-FGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG 335
            V VK   ++    EV    SV  LK+++ QK GIA     L + +  L DD+ L+ Y IQ +S + M  +L+GG
Sbjct:  305 VFVKTLANKTLTIEVKLSNSVLSLKQKVHQKAGIAVNQQILTFGSHTLEDDQKLESYGIQQHSTITMQGRLRGG 378
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BLAST of SMED30033873 vs. Planmine SMEST
Match: SMESG000003398.1 (SMESG000003398.1)

HSP 1 Score: 150.599 bits (379), Expect = 2.837e-48
Identity = 76/77 (98.70%), Postives = 76/77 (98.70%), Query Frame = -3 
Query:  111 MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGGV 341
            MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG V
Sbjct:    1 MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV 77
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BLAST of SMED30033873 vs. Planmine SMEST
Match: SMESG000014648.1 (SMESG000014648.1)

HSP 1 Score: 113.62 bits (283), Expect = 1.056e-33
Identity = 54/77 (70.13%), Postives = 63/77 (81.82%), Query Frame = -3 
Query:  111 MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGGV 341
            MKV VKF +QNF FEVT +T  GDLK QI QKTG+AS  I L YN +YLLDDKPL+KYDIQSN+N+VMIS+L+GG V
Sbjct:    1 MKVFVKFKNQNFTFEVTGETLTGDLKNQIAQKTGMASDQIELMYNVVYLLDDKPLRKYDIQSNANIVMISRLRGGRV 77
[Close]
BLAST of SMED30033873 vs. Planmine SMEST
Match: SMESG000014651.1 (SMESG000014651.1)

HSP 1 Score: 95.5153 bits (236), Expect = 1.635e-26
Identity = 47/77 (61.04%), Postives = 61/77 (79.22%), Query Frame = -3 
Query:  111 MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGGV 341
            MKV V +  Q F FEVTS+T VGDLKKQI QKTG+A  ++ L +N +YLL+DK L+KY+IQ+N+NLV+ISK+ GG V
Sbjct:    1 MKVFVTYNSQIFTFEVTSETLVGDLKKQIVQKTGMAIENLELLFNQVYLLNDKELKKYNIQNNANLVVISKVIGGRV 77
The following BLAST results are available for this feature:
BLAST of SMED30033873 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 SMED30033873 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 SMED30033873 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 SMED30033873 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 SMED30033873 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 SMED30033873 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 SMED30033873 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 SMED30033873 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 SMED30033873 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 SMED30033873 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 2
Match NameE-valueIdentityDescription
ENSPMAT00000006261.11.073e-636.49pep scaffold:Pmarinus_7.0:GL477433:28222:29567:1 g... [more]
ENSPMAT00000006254.12.357e-636.49pep scaffold:Pmarinus_7.0:GL477433:3744:20801:-1 g... [more]
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BLAST of SMED30033873 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 SMED30033873 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 SMED30033873 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 SMED30033873 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000003398.12.837e-4898.70SMESG000003398.1[more]
SMESG000014648.11.056e-3370.13SMESG000014648.1[more]
SMESG000014651.11.635e-2661.04SMESG000014651.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033873 ID=SMED30033873|Name=SMED30033873|organism=Schmidtea mediterranea sexual|type=transcript|length=454bp
TTTTTTTTTTTAATATGAAAATTTATTCTCTAATGAAAAATGAACAAAAA
ACAAATTTATTATAAGCGTTTACTAACGAAGAAAGTTAGCATACATTCCG
TTCCACGTTAAACACCTCCACCTTGGAGTTTACTAATCATAACAAGATTA
GAATTACTTTGGATATCATATTTTTGCAGTGGCTTATCGTCCAATAAATA
AATTGCGTTGTACTGCAAATTAATATCGCCACTAGCAATTCCGGTCTTCT
GGGTGATTTGCTTTTTAAGATCACCAACCGAAGTATCACTAGTAACTTCG
AAAGCAAAGTTTTGGTCTCCAAATTTAACAATGACTTTCATTTTNTAAAN
NNNTNTNAAATANNATANNANNANNANATANNTNNANNTAAATNNNNANN
ANNANANNNATNANNNTGNNNNNNNTNNNAATTNANNNTATATTTAGAGT
GTCA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR000626Ubiquitin-like_dom
IPR029071Ubiquitin-like_domsf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000626Ubiquitin-like domainSMARTSM00213ubq_7coord: 1..71
e-value: 3.4E-11
score: 53.2
IPR000626Ubiquitin-like domainPFAMPF00240ubiquitincoord: 4..71
e-value: 8.0E-13
score: 47.9
IPR000626Ubiquitin-like domainPROSITEPS50053UBIQUITIN_2coord: 1..75
score: 15.688
NoneNo IPR availableGENE3DG3DSA:3.10.20.90coord: 1..69
e-value: 6.2E-15
score: 56.9
NoneNo IPR availableCDDcd17039Ubl_ubiquitin_likecoord: 3..69
e-value: 1.76046E-12
score: 54.5246
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 1..75