SMED30017182

Overview
NameSMED30017182
Smed IDSMED30017182
Length (bp)1317
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 SMED30017182 (SMED30017182) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017182 (SMED30017182) 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 SMED30017182 (SMED30017182) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017182 (SMED30017182) 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



SMED30017182

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
head regionSMED30017182h1SMcG0000456 SmedASXL_001184SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30017182h1SMcG0000456 SmedASXL_019592SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30017182h1SMcG0000456 dd_Smed_v4_22356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30017182h1SMcG0000456 dd_Smed_v4_22356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30017182h1SMcG0000456 dd_Smed_v6_22356_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
photoreceptor neuronSMED30017182h1SMcG0000456 SMED30017182smed_20140614PMID:22884275
Lapan et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
pigment cellSMED30017182h1SMcG0000456 SMED30017182smed_20140614PMID:22884275
Lapan et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30017182 vs. Ensembl Zebrafish
Match: ghsra (growth hormone secretagogue receptor a [Source:ZFIN;Acc:ZDB-GENE-070912-238])

HSP 1 Score: 48.521 bits (114), Expect = 8.543e-6
Identity = 30/84 (35.71%), Postives = 49/84 (58.33%), Query Frame = 1 
Query:  730 HTKLDVQQHKIISLVVFFQILTWIPFLIS--LILLHCEFDLPVLAV--HFLSLST----QLNGAFNPLIYAIFSKKYRVFYCRL 957
              K + Q  K++++VVF  +L W+PF +   LI    E   PV+++  H+ +L +     L+ A NP++Y I SKKYR+  C+L
Sbjct:  248 RDKSNRQTVKMLAVVVFAFVLCWLPFHVGRYLISKSTEMGSPVMSIISHYCNLISFVLFYLSAAINPILYNIMSKKYRMAACKL 331
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BLAST of SMED30017182 vs. Ensembl Xenopus
Match: GHSR (growth hormone secretagogue receptor [Source:NCBI gene;Acc:100497774])

HSP 1 Score: 50.0618 bits (118), Expect = 4.444e-6
Identity = 34/94 (36.17%), Postives = 49/94 (52.13%), Query Frame = 1 
Query:  727 RHTKLDVQQHKIISLVVFFQILTWIPFLISLILLHCEFDLPVLAVHFLSLSTQL--------NGAFNPLIYAIFSKKYRVFYCRL--IPQTFRK 978
            +H K   Q  K++++VVF  IL W+PF ++  L    F+   L +  +S    L        + A NP++Y I SKKYRV  CRL  + Q  RK
Sbjct:  254 KHNK---QTVKMLAVVVFAFILCWLPFHVARYLFSKSFEAGSLEIALISQYCNLVSFVLFYLSAAINPILYNIMSKKYRVAACRLFRLKQVSRK 344
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BLAST of SMED30017182 vs. Planmine SMEST
Match: SMESG000017559.1 (SMESG000017559.1)

HSP 1 Score: 535.413 bits (1378), Expect = 0.000e+0
Identity = 340/349 (97.42%), Postives = 342/349 (97.99%), Query Frame = 1 
Query:   37 MFLTNITYFEMIPSPLKEISGSMTVVINIILVSTNTVCMLSLICSIFHKSKSIGIFDFYIMLLSGIDILESLIPGIIWVIYEFSNPHSIESISCIIYRSTVNTFQILSLSIIFCVTFFCCLKKLNINNPIVFLRFFLLSLFATXXXXXXXXXXXXXXXXXXXXXXWICLQGILIHVNKSKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKPRPTNPGIYTVHQSRPVDYRHTKLDVQQHKIISLVVFFQILTWIPFLISLILLHCEFDLPVLAVHFLSLSTQLNGAFNPLIYAIFSKKYRVFYCRLIPQTFRKKANFYKLNKNLGKSYFHRPLFPTDFSLSTKTASNF 1083
            MFLTNITYFEMIPSPLKEISGSMTVVINIILVSTNTVCMLSLICSIFHKSKSIGIFDFYIMLLSGIDILESLIPGIIWVIYEFSNPHSIESISCIIYRSTVNTFQILSLSIIFCVTFFCCLKKLNIN+PIVFLRFFLLSLFATSFIALIFFILPLTTTTSFSTSSWICLQGILIHVNKSKITTIQLLLFLSISTILIIGIILSLTLILLIKPRPTNPGIYTVHQSRPVDYRHTKLDVQQHKIISLVVFFQILTWIPFLISLILLHCEFDLPVLAVHFLSLSTQLNGAFNPLIYAIFSKKYRVFYCRLIPQTFRKKANFYKLNKNLGKSYFHRPLFPTDF    K  + F
Sbjct:    1 MFLTNITYFEMIPSPLKEISGSMTVVINIILVSTNTVCMLSLICSIFHKSKSIGIFDFYIMLLSGIDILESLIPGIIWVIYEFSNPHSIESISCIIYRSTVNTFQILSLSIIFCVTFFCCLKKLNINDPIVFLRFFLLSLFATSFIALIFFILPLTTTTSFSTSSWICLQGILIHVNKSKITTIQLLLFLSISTILIIGIILSLTLILLIKPRPTNPGIYTVHQSRPVDYRHTKLDVQQHKIISLVVFFQILTWIPFLISLILLHCEFDLPVLAVHFLSLSTQLNGAFNPLIYAIFSKKYRVFYCRLIPQTFRKKANFYKLNKNLGKSYFHRPLFPTDFYYRQKLRAIF 349
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BLAST of SMED30017182 vs. Planmine SMEST
Match: SMESG000017559.1 (SMESG000017559.1)

HSP 1 Score: 514.998 bits (1325), Expect = 0.000e+0
Identity = 330/339 (97.35%), Postives = 332/339 (97.94%), Query Frame = 1 
Query:   67 MIPSPLKEISGSMTVVINIILVSTNTVCMLSLICSIFHKSKSIGIFDFYIMLLSGIDILESLIPGIIWVIYEFSNPHSIESISCIIYRSTVNTFQILSLSIIFCVTFFCCLKKLNINNPIVFLRFFLLSLFATXXXXXXXXXXXXXXXXXXXXXXWICLQGILIHVNKSKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKPRPTNPGIYTVHQSRPVDYRHTKLDVQQHKIISLVVFFQILTWIPFLISLILLHCEFDLPVLAVHFLSLSTQLNGAFNPLIYAIFSKKYRVFYCRLIPQTFRKKANFYKLNKNLGKSYFHRPLFPTDFSLSTKTASNF 1083
            MIPSPLKEISGSMTVVINIILVSTNTVCMLSLICSIFHKSKSIGIFDFYIMLLSGIDILESLIPGIIWVIYEFSNPHSIESISCIIYRSTVNTFQILSLSIIFCVTFFCCLKKLNIN+PIVFLRFFLLSLFATSFIALIFFILPLTTTTSFSTSSWICLQGILIHVNKSKITTIQLLLFLSISTILIIGIILSLTLILLIKPRPTNPGIYTVHQSRPVDYRHTKLDVQQHKIISLVVFFQILTWIPFLISLILLHCEFDLPVLAVHFLSLSTQLNGAFNPLIYAIFSKKYRVFYCRLIPQTFRKKANFYKLNKNLGKSYFHRPLFPTDF    K  + F
Sbjct:    1 MIPSPLKEISGSMTVVINIILVSTNTVCMLSLICSIFHKSKSIGIFDFYIMLLSGIDILESLIPGIIWVIYEFSNPHSIESISCIIYRSTVNTFQILSLSIIFCVTFFCCLKKLNINDPIVFLRFFLLSLFATSFIALIFFILPLTTTTSFSTSSWICLQGILIHVNKSKITTIQLLLFLSISTILIIGIILSLTLILLIKPRPTNPGIYTVHQSRPVDYRHTKLDVQQHKIISLVVFFQILTWIPFLISLILLHCEFDLPVLAVHFLSLSTQLNGAFNPLIYAIFSKKYRVFYCRLIPQTFRKKANFYKLNKNLGKSYFHRPLFPTDFYYRQKLRAIF 339
The following BLAST results are available for this feature:
BLAST of SMED30017182 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 SMED30017182 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 SMED30017182 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 SMED30017182 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ghsra8.543e-635.71growth hormone secretagogue receptor a [Source:ZFI... [more]
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BLAST of SMED30017182 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
GHSR4.444e-636.17growth hormone secretagogue receptor [Source:NCBI ... [more]
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BLAST of SMED30017182 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 SMED30017182 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 SMED30017182 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 SMED30017182 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 SMED30017182 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 SMED30017182 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 SMED30017182 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 SMED30017182 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 SMED30017182 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000017559.10.000e+097.42SMESG000017559.1[more]
SMESG000017559.10.000e+097.35SMESG000017559.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017182 ID=SMED30017182|Name=SMED30017182|organism=Schmidtea mediterranea sexual|type=transcript|length=1317bp
AATGGAAAATAAATTTGTCAAAGTCTTTTCGAAAATATGTTTCTGACAAA
TATCACGTATTTCGAGATGATCCCGTCTCCATTGAAAGAAATTTCAGGAT
CAATGACAGTCGTGATCAACATTATTTTGGTGTCAACGAACACAGTTTGT
ATGCTGTCATTAATTTGTTCGATTTTTCACAAATCAAAAAGCATTGGAAT
CTTTGATTTCTACATTATGCTACTGTCAGGAATCGATATTTTGGAATCTC
TAATTCCTGGAATTATTTGGGTGATTTATGAATTCAGCAATCCTCACAGT
ATTGAATCCATCTCTTGCATAATTTATAGGTCAACAGTGAATACCTTTCA
AATTCTTTCACTGTCTATCATATTTTGTGTGACGTTTTTTTGCTGTTTAA
AAAAACTGAATATCAACAATCCAATTGTGTTTCTTCGATTCTTTTTACTT
TCTCTTTTCGCCACTAGTTTTATTGCTTTGATATTTTTCATATTACCGTT
GACAACAACGACATCGTTCTCAACTAGCTCTTGGATTTGTTTGCAAGGAA
TTCTTATTCACGTTAACAAATCTAAAATCACGACAATTCAGTTGCTTTTA
TTTCTTTCTATTTCTACTATTTTAATTATTGGTATTATTCTATCGCTGAC
TCTTATTTTACTCATTAAGCCACGCCCAACAAATCCAGGAATTTATACAG
TCCATCAATCTCGCCCCGTCGATTATCGTCACACCAAACTAGATGTTCAA
CAACACAAAATTATTAGCTTAGTAGTTTTTTTCCAAATACTCACCTGGAT
TCCATTTTTAATATCATTGATTTTGCTTCACTGTGAATTCGACTTACCAG
TGCTGGCTGTTCATTTTCTCAGCTTATCAACTCAACTGAATGGGGCTTTT
AATCCACTAATCTATGCAATTTTCTCCAAAAAATATCGAGTATTCTATTG
CAGGCTGATTCCTCAAACATTTAGAAAGAAAGCCAATTTTTATAAGCTCA
ATAAAAATCTCGGCAAATCTTACTTTCATCGGCCATTATTTCCCACTGAT
TTTTCATTATCGACAAAAACTGCGAGCAATTTTCCTGGAGCACTTCAATC
GCAAACGATAACCGAAAATTTGGTATTATACGCTAAATGCCACGAAACTG
ATTGCGATGCCGTTGGAAAAGAAATGATTATGCGCCGTTTTCTTGAGGAT
AATCCAATTTTTGATACCGTCGAGTGACATTGTTACTCATTATTATCTTT
TCTGCTCCACTTCACTTAAATCGATGATAAAATTTAATAACATTTATTGT
AATAATAAATATTTACA
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protein sequence of SMED30017182-orf-1

>SMED30017182-orf-1 ID=SMED30017182-orf-1|Name=SMED30017182-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=397bp
MFLTNITYFEMIPSPLKEISGSMTVVINIILVSTNTVCMLSLICSIFHKS
KSIGIFDFYIMLLSGIDILESLIPGIIWVIYEFSNPHSIESISCIIYRST
VNTFQILSLSIIFCVTFFCCLKKLNINNPIVFLRFFLLSLFATSFIALIF
FILPLTTTTSFSTSSWICLQGILIHVNKSKITTIQLLLFLSISTILIIGI
ILSLTLILLIKPRPTNPGIYTVHQSRPVDYRHTKLDVQQHKIISLVVFFQ
ILTWIPFLISLILLHCEFDLPVLAVHFLSLSTQLNGAFNPLIYAIFSKKY
RVFYCRLIPQTFRKKANFYKLNKNLGKSYFHRPLFPTDFSLSTKTASNFP
GALQSQTITENLVLYAKCHETDCDAVGKEMIMRRFLEDNPIFDTVE*
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Aliases
The feature 'SMED30017182' has the following synonyms
Synonym
Smed-59sley
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000017photoreceptor neuron
PLANA:0000418head
PLANA:0002075pigment cell
Vocabulary: INTERPRO
TermDefinition
IPR017452GPCR_Rhodpsn_7TM
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane