SMED30007246

Overview
NameSMED30007246
Smed IDSMED30007246
Length (bp)660
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 SMED30007246 (SMED30007246) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007246 (SMED30007246) 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 SMED30007246 (SMED30007246) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007246 (SMED30007246) 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



SMED30007246

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30007246h1SMcG0004733 Contig3259GPL15192PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30007246h1SMcG0004733 Contig3259GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30007246h1SMcG0004733 dd_Smed_v4_797_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30007246h1SMcG0004733 dd_Smed_v4_797_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007246h1SMcG0004733 dd_Smed_v4_797_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007246h1SMcG0004733 dd_Smed_v4_797_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007246h1SMcG0004733 dd_Smed_v4_797_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
Alignments
SMED30007246 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003898:50264..51010 +3198
v31.003258:9603..10351 -3188
Homology
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BLAST of SMED30007246 vs. TrEMBL
Match: A0A267F9X9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig026293g1 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 5.791e-6
Identity = 41/114 (35.96%), Postives = 58/114 (50.88%), Query Frame = 2 
Query:   86 MALP-ITIPRILLFIFLVAIACSIISVATDSY------LFDKRNSDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYG 406
            MA P IT  +I +      IACSI S AT ++      LFD  N     T  AF +I +  L F ++MEIL     +FK +R + +L     +L+  SL+IS  + S R+  YG
Sbjct:    1 MAAPRITFHQITIITLCFGIACSIASCATRAWQSGSGGLFDLPNEAWANTIKAFAIIGVAMLGFSLLMEILMVASNTFKLSRAMHLLCFICCLLSAASLLISLGLYS-RHYSYG 113
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BLAST of SMED30007246 vs. TrEMBL
Match: A0A267EGW5 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig016342g1 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 6.360e-6
Identity = 41/112 (36.61%), Postives = 57/112 (50.89%), Query Frame = 2 
Query:   86 MALP-ITIPRILLFIFLVAIACSIISVATDSY----LFDKRNSDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYG 406
            MA P IT  +I +      IACSI S AT ++    LFD  N     T  AF +I +  L F + MEIL     +FK +R + +L     +L+  SL+IS  + S R+  YG
Sbjct:    1 MAAPRITFHQITIITLCFGIACSIASCATRAWKSGGLFDLPNEAWANTIKAFAIIGVAMLGFSLFMEILMVASNTFKLSRAMHLLCFICCLLSAASLLISLGLYS-RHYSYG 111
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BLAST of SMED30007246 vs. Planmine SMEST
Match: SMESG000045656.1 (SMESG000045656.1)

HSP 1 Score: 256.529 bits (654), Expect = 2.489e-88
Identity = 130/130 (100.00%), Postives = 130/130 (100.00%), Query Frame = 2 
Query:   86 MALPITIPRILLFIFLVAIACSIISVATDSYLFDKRNSDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYGWTVAACTLVMEALVIAFFHHFFM 475
            MALPITIPRILLFIFLVAIACSIISVATDSYLFDKRNSDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYGWTVAACTLVMEALVIAFFHHFFM
Sbjct:    1 MALPITIPRILLFIFLVAIACSIISVATDSYLFDKRNSDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYGWTVAACTLVMEALVIAFFHHFFM 130
[Close]
BLAST of SMED30007246 vs. Planmine SMEST
Match: SMESG000045652.1 (SMESG000045652.1)

HSP 1 Score: 136.346 bits (342), Expect = 6.325e-41
Identity = 65/128 (50.78%), Postives = 93/128 (72.66%), Query Frame = 2 
Query:   89 ALPITIPRILLFIFLVAIACSIISVATDSYLFDKRNSDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYGWTVAACTLVMEALVIAFFHHFF 472
            A+ +   ++LLFIF++A+ C IIS+ATD YLF K NS   K Y AFL+I I+AL+ V+++E+L +FI S ++N  ++I+ + AMV+  V LII+CAV ++ N PYGWTVA CTLV+EA+VI    HF 
Sbjct:    5 AVIVQTQKVLLFIFVIALCCCIISMATDPYLFGKYNSLNMKLYTAFLIIGIVALIVVVLLEMLRAFISSVRSNGSIQIVGIVAMVIAAVCLIIACAVYNDGNVPYGWTVAGCTLVIEAVVIILITHFL 132
[Close]
BLAST of SMED30007246 vs. Planmine SMEST
Match: SMESG000015329.1 (SMESG000015329.1)

HSP 1 Score: 128.642 bits (322), Expect = 6.990e-38
Identity = 62/115 (53.91%), Postives = 89/115 (77.39%), Query Frame = 2 
Query:  107 PRILLFIFLVAIACSIISVATDSYLFDKRNSDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYGWTVAACTLVMEALVI 451
            P+I+L IF +++ C+II++ATDS LF    SDR K Y +FL+I+II+L  V+ +E+L +F+ S   NRI++ILS+A MVL GVSLIISC++ S  + PYGWTVA+CTL+ME ++I
Sbjct:    7 PKIMLIIFAMSLVCAIIAIATDSSLFSY--SDRNKAYGSFLIIAIISLGIVLFIELLLNFVGSLSENRIMQILSIAFMVLAGVSLIISCSIYSTSHMPYGWTVASCTLIMEGILI 119
[Close]
BLAST of SMED30007246 vs. Planmine SMEST
Match: SMESG000045652.1 (SMESG000045652.1)

HSP 1 Score: 114.39 bits (285), Expect = 1.028e-32
Identity = 54/103 (52.43%), Postives = 74/103 (71.84%), Query Frame = 2 
Query:  164 ATDSYLFDKRNSDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYGWTVAACTLVMEALVIAFFHHFF 472
            ATD YLF K NS   K Y AFL+I I+AL+ V+++E+L +FI S ++N  ++I+ + AMV+  V LII+CAV ++ N PYGWTVA CTLV+EA+VI    HF 
Sbjct:    2 ATDPYLFGKYNSLNMKLYTAFLIIGIVALIVVVLLEMLRAFISSVRSNGSIQIVGIVAMVIAAVCLIIACAVYNDGNVPYGWTVAGCTLVIEAVVIILITHFL 104
[Close]
BLAST of SMED30007246 vs. Planmine SMEST
Match: SMESG000015390.1 (SMESG000015390.1)

HSP 1 Score: 110.153 bits (274), Expect = 8.666e-31
Identity = 63/124 (50.81%), Postives = 90/124 (72.58%), Query Frame = 2 
Query:   98 ITIPRILLFIFLVAIACSIISVATDSYLFDKRNSDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYGWTVAACTLVMEALVIAFFHHF 469
            ++I ++ L IF+++ AC+II++ TD+       SDR K Y AFL+I II+L  V+VMEIL +FI SF  NRI++ILS++ MV+ GV+LII+CA+    + PYGWTVA+CTL+MEA+ I  F  F
Sbjct:    4 VSIGKVSLTIFILSFACAIIAICTDAGKLHSY-SDRDKAYGAFLIIGIISLGIVVVMEILLNFIHSFTDNRIIQILSLSFMVIGGVALIIACAICFPMHFPYGWTVASCTLLMEAIFIFIFLRF 126
The following BLAST results are available for this feature:
BLAST of SMED30007246 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 SMED30007246 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 SMED30007246 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 SMED30007246 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 SMED30007246 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 SMED30007246 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 SMED30007246 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 SMED30007246 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A267F9X95.791e-635.96Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267EGW56.360e-636.61Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30007246 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 SMED30007246 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 SMED30007246 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 SMED30007246 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 SMED30007246 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 SMED30007246 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000045656.12.489e-88100.00SMESG000045656.1[more]
SMESG000045652.16.325e-4150.78SMESG000045652.1[more]
SMESG000015329.16.990e-3853.91SMESG000015329.1[more]
SMESG000045652.11.028e-3252.43SMESG000045652.1[more]
SMESG000015390.18.666e-3150.81SMESG000015390.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007246 ID=SMED30007246|Name=SMED30007246|organism=Schmidtea mediterranea sexual|type=transcript|length=660bp
AGAACATTCAGGTAATCAAAATTGAGTGAACGATTTCATGATTCTAATAA
TAATTTCAAACAGTTTTATTATTTAGAAATCGTAAATGGCCTTACCGATT
ACCATTCCTAGAATTTTATTATTTATATTTCTTGTCGCAATCGCTTGTAG
CATAATTTCTGTCGCAACAGATTCATATTTATTTGATAAAAGAAATTCTG
ATCGAAGAAAAACCTATGCCGCATTTCTAGTCATTTCAATCATTGCTTTG
GTATTTGTAATAGTTATGGAGATTTTAACGTCATTTATTGAATCGTTTAA
AACTAATCGAATCCTGAAAATCCTTTCCGTTGCTGCAATGGTTTTAACGG
GAGTAAGTCTAATAATTTCTTGTGCTGTTGTCAGTGAGAGAAACAATCCT
TACGGATGGACGGTGGCCGCTTGCACTCTGGTTATGGAAGCTCTTGTGAT
TGCATTCTTTCACCATTTCTTCATGTGAAACAAATTGGTGAATAATTTAT
TTTGATAAATAATTTCAATAACTGATTTGAATGGTTTGTTTATATACTTT
AAAGTGTGGATTATTTTTTGAAACGATTCTAAAATTTGTTTTAAAGTGTC
TTTTATTTCCATTTCACTGATTTTAATCTTTCAATAATTTGATTTTTTTT
CTGTTAAAAA
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protein sequence of SMED30007246-orf-1

>SMED30007246-orf-1 ID=SMED30007246-orf-1|Name=SMED30007246-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=131bp
MALPITIPRILLFIFLVAIACSIISVATDSYLFDKRNSDRRKTYAAFLVI
SIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVS
ERNNPYGWTVAACTLVMEALVIAFFHHFFM*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 77..99
NoneNo IPR availableTMHMMTMhelixcoord: 45..67
NoneNo IPR availableTMHMMTMhelixcoord: 10..32
NoneNo IPR availableTMHMMTMhelixcoord: 106..128