SMED30034249

Overview
NameSMED30034249
Smed IDSMED30034249
Length (bp)2392
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 SMED30034249 (SMED30034249) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034249 (SMED30034249) 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 SMED30034249 (SMED30034249) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034249 (SMED30034249) 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



SMED30034249

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



PAGE Curations: 15

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30034249h1SMcG0015704 Contig52624uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034249h1SMcG0015704 Contig52624newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034249h1SMcG0015704 Contig36943newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034249h1SMcG0015704 Contig36943uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30034249h1SMcG0015704 dd_Smed_v4_8345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30034249h1SMcG0015704 dd_Smed_v4_8345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30034249h1SMcG0015704 dd_Smed_v4_8345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30034249h1SMcG0015704 dd_Smed_v4_8345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034249h1SMcG0015704 dd_Smed_v4_8345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30034249h1SMcG0015704 dd_Smed_v4_8345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
non-ciliated neuronSMED30034249h1SMcG0015704 dd_Smed_v4_8345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30034249h1SMcG0015704 dd_Smed_v4_8345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30034249h1SMcG0015704 dd_Smed_v6_8345_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
protonephridiaSMED30034249h1SMcG0015704 dd_Smed_v6_8345_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30034249h1SMcG0015704 dd_Smed_v4_8345_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
SMED30034249 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000696:63641..76601 +10874
Homology
[Close]
BLAST of SMED30034249 vs. Planmine SMEST
Match: SMESG000042496.1 (SMESG000042496.1)

HSP 1 Score: 1299.65 bits (3362), Expect = 0.000e+0
Identity = 724/748 (96.79%), Postives = 729/748 (97.46%), Query Frame = 3 
Query:  114 MTDIKIDTFRSSVYDKEFSGSETESETIDDFSQYSDQMNNVISDKSFNDSHSTTPISKVIPIKINGNDNQIHLHDYLDSSLNEEKDTSEDLMVQXXXXXXXXXXXXXXXLVNGVKQASEFEEYIIHDSHSDGNTNKSKCDKFYKNQTNLDFEQAMNGNYLNETPLDKSRNENDCCIDETIEATKAHSSLHGRTIYDKSSESSISETNEKSKIFLLSKENNIEKFQTHMPQNEQEINNKNPKIQENSNSGKXXXXXXXXXXXXXXXXXXXXKGEHSIISEPITTSQMKEKNLNKSNNRVSILKNDKTIEKXXXXXXXXXXXXXXXXXXXXKRHFIYFKSQDPHKTDYKFHNRKDYLHDKQKFTTYKRREKYNLYKNAHQKNIDECDNIKSKSLQSKTQFHDRNNKKIDTETAVKHMKWVDPFRSYHLKYDLKDNGRSMQHWIRRKQDALYRSDPKNNVENSIGKKGIKCRSTNFAKSYSKIPHTHKSNSQKDIKEFIIRGNIKESLFQIRHPYPTFAEQEYIFYSPTNKRASEYFEFNEDIDFESLGFYNLNQDELKPKQRLLDSKKGTRNNLSNEVSQILNKFETQEKGMQQKSKNLRERRNDEEMTYTHRNCHLPVSCCINSCCYSTPCSCLFRKGKVFERYKYLSYERVGEKVKGECQAXXXXXXXXXXXXXXXIEKKIDNKSKRSNKIDYLEAQLEQIEDKIRNINSNGEKSVFQCTMDLECQCXXXXXXXXXXXXVPRSIREAA 2357
            MTDIKIDTFRSSVYDKEFSGSETESETIDDFSQYSDQMNNVISDKS NDSHSTTPISKVIPIKINGNDNQIHLHDYLDSSLNEEKD SEDLMVQISKKTTIKKIISKTTLVNGVKQASEFEEYIIHDSHSDGNTNKSKCDKFYKNQTNLDFEQAMNGNYLN TPLDKSRNENDCCIDETIEATKAHSSLHGRTIYDKSSESSISETNEKSKIFLLSKENNIEKFQTHMPQNEQEINNKNP+IQENSNSGKINENINEIQHQNLNENENNNK EH IISEPITTS MKEKNLNKSNN VSILKNDKTIEKNQKINTNINDL N+      KRHFIYFKSQDPHKTDYKFHNRKDY+HDKQKFTTYKRREK NLYKN HQKNIDECDNIKSKSLQSKTQFHDRNNKKIDTETAVKHMKWVDPFRSYHLKYDLKDNGRSMQHWIRRKQDALYRSDPKNNVENSIGKKGIKCRSTNFAKSYSK+PHTHKSNSQKDIKEFIIRGNIKE+LFQIRHPYPTFAEQEYIFYSPTNKRASEYFEFNEDIDFESLGFYNLNQDELKPKQRLLDSKKGTRNNLSNEVSQILNKFETQEKGMQQKSKNLRERRNDEEM YTHRNCHLPVSCCINSCCYSTPCSCLFRKGKVFERYKYLSYERVGEKVKGECQATEYYEDSETSET TYIEKKIDNKSKRSNKIDYLEAQLEQIEDKIRNINSNGEKSVFQC MDLECQCREIERELEYLYRVPRSIREAA
Sbjct:    1 MTDIKIDTFRSSVYDKEFSGSETESETIDDFSQYSDQMNNVISDKSLNDSHSTTPISKVIPIKINGNDNQIHLHDYLDSSLNEEKDPSEDLMVQISKKTTIKKIISKTTLVNGVKQASEFEEYIIHDSHSDGNTNKSKCDKFYKNQTNLDFEQAMNGNYLNGTPLDKSRNENDCCIDETIEATKAHSSLHGRTIYDKSSESSISETNEKSKIFLLSKENNIEKFQTHMPQNEQEINNKNPEIQENSNSGKINENINEIQHQNLNENENNNKEEHLIISEPITTSPMKEKNLNKSNNTVSILKNDKTIEKNQKINTNINDLKND------KRHFIYFKSQDPHKTDYKFHNRKDYIHDKQKFTTYKRREKDNLYKNDHQKNIDECDNIKSKSLQSKTQFHDRNNKKIDTETAVKHMKWVDPFRSYHLKYDLKDNGRSMQHWIRRKQDALYRSDPKNNVENSIGKKGIKCRSTNFAKSYSKVPHTHKSNSQKDIKEFIIRGNIKENLFQIRHPYPTFAEQEYIFYSPTNKRASEYFEFNEDIDFESLGFYNLNQDELKPKQRLLDSKKGTRNNLSNEVSQILNKFETQEKGMQQKSKNLRERRNDEEMAYTHRNCHLPVSCCINSCCYSTPCSCLFRKGKVFERYKYLSYERVGEKVKGECQATEYYEDSETSETDTYIEKKIDNKSKRSNKIDYLEAQLEQIEDKIRNINSNGEKSVFQCAMDLECQCREIERELEYLYRVPRSIREAA 742
The following BLAST results are available for this feature:
BLAST of SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 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 SMED30034249 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000042496.10.000e+096.79SMESG000042496.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034249 ID=SMED30034249|Name=SMED30034249|organism=Schmidtea mediterranea sexual|type=transcript|length=2392bp
TAACAATTAATTAGCTATGCTCCATTGTCAGTACAAACCTGACGGTTTCA
TTGGTGTCTTGACAACAAATTAGAATAATCAATATCAATTCAGAATTCTC
GAGCTGCATTTAAATGACTGATATAAAGATTGATACATTCCGCTCGTCTG
TTTACGATAAAGAATTTTCTGGTTCGGAAACCGAAAGTGAAACCATTGAC
GATTTTTCACAATATAGTGATCAAATGAATAACGTCATTTCGGATAAATC
ATTCAATGATTCTCATTCTACAACTCCGATTTCAAAAGTGATTCCAATAA
AAATTAATGGCAATGATAACCAAATCCATTTGCATGATTATTTGGATTCC
TCTTTGAATGAAGAAAAAGATACTTCAGAAGATTTAATGGTTCAAATATC
GAAAAAGACCACAATTAAAAAAATCATATCAAAGACGACATTAGTAAATG
GAGTTAAACAAGCAAGTGAGTTTGAAGAGTATATTATTCACGATAGCCAT
TCGGATGGGAATACTAATAAATCAAAATGCGATAAATTCTATAAAAATCA
AACCAATCTTGATTTCGAGCAGGCAATGAATGGTAATTATTTAAACGAAA
CCCCCCTAGATAAATCCCGCAATGAAAATGATTGTTGTATTGATGAAACT
ATTGAAGCTACTAAAGCTCACAGTTCTTTACATGGAAGAACAATTTATGA
CAAAAGTTCAGAATCGTCTATATCTGAAACCAATGAAAAATCAAAAATAT
TTTTATTGTCCAAAGAAAATAATATTGAAAAGTTTCAAACTCATATGCCA
CAGAATGAACAGGAAATTAACAATAAAAATCCAAAAATTCAAGAAAATTC
AAATTCTGGTAAAATAAATGAAAATATCAATGAAATTCAACATCAAAATC
TGAATGAAAACGAAAACAATAATAAAGGGGAGCATTCAATCATTTCCGAA
CCAATCACAACTTCACAAATGAAAGAAAAAAACCTAAATAAATCAAATAA
TAGAGTTTCCATATTAAAAAATGATAAAACCATTGAAAAAAATCAGAAAA
TCAACACGAATATTAATGATTTGAACAATAACATGGAAATGAAGAATGAC
AAAAGACATTTTATTTACTTTAAAAGTCAAGATCCTCACAAAACCGATTA
TAAATTTCACAATAGAAAAGATTACTTACATGATAAGCAGAAATTTACCA
CGTATAAACGAAGGGAAAAATATAATCTATATAAAAATGCTCATCAAAAA
AACATTGATGAATGTGATAACATTAAATCCAAATCTTTGCAGTCAAAAAC
ACAATTTCATGACAGAAATAATAAAAAAATTGATACAGAAACTGCTGTAA
AGCATATGAAATGGGTTGATCCATTTAGGTCATATCATTTGAAATATGAT
TTGAAAGATAATGGAAGATCAATGCAACACTGGATAAGACGTAAGCAAGA
CGCTTTATATCGATCAGATCCCAAAAATAATGTAGAAAATTCAATTGGCA
AAAAAGGAATAAAATGTAGGTCTACTAACTTCGCAAAATCTTATTCCAAA
ATTCCTCATACTCACAAATCCAATTCTCAGAAAGATATTAAAGAATTTAT
CATTCGTGGAAATATAAAGGAGAGCTTATTTCAAATAAGGCACCCTTATC
CTACATTTGCAGAGCAAGAATATATTTTCTATTCTCCAACAAACAAAAGA
GCATCGGAATATTTCGAATTCAACGAAGATATAGATTTTGAATCATTAGG
TTTTTACAATTTAAATCAAGATGAATTAAAACCTAAACAGCGATTACTTG
ATTCTAAAAAAGGGACAAGAAACAATCTTTCTAATGAAGTTTCACAGATT
TTAAACAAGTTTGAAACTCAAGAAAAAGGTATGCAACAAAAGTCAAAAAA
TTTAAGAGAGCGCAGAAATGATGAAGAAATGACTTATACCCACAGAAATT
GTCACCTACCCGTTTCTTGTTGCATCAACAGTTGTTGCTATTCCACACCG
TGCAGTTGTTTATTCAGAAAAGGTAAAGTATTTGAAAGATACAAATATTT
GTCTTATGAGAGAGTAGGCGAAAAAGTCAAAGGAGAGTGTCAAGCAACTG
AATATTATGAAGACTCGGAAACATCAGAAACACACACTTATATTGAAAAA
AAAATCGATAATAAAAGTAAAAGAAGCAATAAAATTGATTATTTAGAAGC
ACAATTAGAACAAATCGAAGACAAAATCCGTAATATAAATTCAAATGGCG
AAAAAAGTGTTTTTCAATGCACTATGGATTTAGAGTGCCAATGTCGAGAA
ATTGAGCGAGAACTGGAATATTTATATAGAGTCCCAAGAAGCATCAGAGA
AGCAGCATAACAATAAATCAGAGATTGCCAAGAATTTATACA
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protein sequence of SMED30034249-orf-1

>SMED30034249-orf-1 ID=SMED30034249-orf-1|Name=SMED30034249-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=749bp
MTDIKIDTFRSSVYDKEFSGSETESETIDDFSQYSDQMNNVISDKSFNDS
HSTTPISKVIPIKINGNDNQIHLHDYLDSSLNEEKDTSEDLMVQISKKTT
IKKIISKTTLVNGVKQASEFEEYIIHDSHSDGNTNKSKCDKFYKNQTNLD
FEQAMNGNYLNETPLDKSRNENDCCIDETIEATKAHSSLHGRTIYDKSSE
SSISETNEKSKIFLLSKENNIEKFQTHMPQNEQEINNKNPKIQENSNSGK
INENINEIQHQNLNENENNNKGEHSIISEPITTSQMKEKNLNKSNNRVSI
LKNDKTIEKNQKINTNINDLNNNMEMKNDKRHFIYFKSQDPHKTDYKFHN
RKDYLHDKQKFTTYKRREKYNLYKNAHQKNIDECDNIKSKSLQSKTQFHD
RNNKKIDTETAVKHMKWVDPFRSYHLKYDLKDNGRSMQHWIRRKQDALYR
SDPKNNVENSIGKKGIKCRSTNFAKSYSKIPHTHKSNSQKDIKEFIIRGN
IKESLFQIRHPYPTFAEQEYIFYSPTNKRASEYFEFNEDIDFESLGFYNL
NQDELKPKQRLLDSKKGTRNNLSNEVSQILNKFETQEKGMQQKSKNLRER
RNDEEMTYTHRNCHLPVSCCINSCCYSTPCSCLFRKGKVFERYKYLSYER
VGEKVKGECQATEYYEDSETSETHTYIEKKIDNKSKRSNKIDYLEAQLEQ
IEDKIRNINSNGEKSVFQCTMDLECQCREIERELEYLYRVPRSIREAA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 574..594
NoneNo IPR availableCOILSCoilCoilcoord: 303..323
NoneNo IPR availableCOILSCoilCoilcoord: 678..705