SMED30014876

Overview
NameSMED30014876
Smed IDSMED30014876
Length (bp)737
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 SMED30014876 (SMED30014876) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014876 (SMED30014876) 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 SMED30014876 (SMED30014876) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014876 (SMED30014876) 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




SMED30014876

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
pigment cellSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 SmedASXL_010535SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 SmedASXL_010535SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 SmedASXL_010535SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v4_61_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v4_61_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v4_61_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v4_61_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v4_61_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v4_61_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v4_61_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v4_61_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 Contig55562uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 Contig55562newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Category 2 cellSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v6_61_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30014876SMESG000054780.1 SMESG000025014.1 SMESG000025004.1 dd_Smed_v4_61_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
SMED30014876 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.027295:4542..5329 +3602
v31.012923:4389..5176 +3585
Homology
BLAST of SMED30014876 vs. Planmine SMEST
Match: SMESG000054780.1 (SMESG000054780.1)

HSP 1 Score: 272.322 bits (695), Expect = 6.359e-94
Identity = 139/139 (100.00%), Postives = 139/139 (100.00%), Query Frame = 1
Query:  301 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECGKSR 717
            MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECGKSR
Sbjct:    1 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECGKSR 139          
BLAST of SMED30014876 vs. Planmine SMEST
Match: SMESG000025014.1 (SMESG000025014.1)

HSP 1 Score: 272.322 bits (695), Expect = 6.359e-94
Identity = 139/139 (100.00%), Postives = 139/139 (100.00%), Query Frame = 1
Query:  301 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECGKSR 717
            MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECGKSR
Sbjct:    1 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECGKSR 139          
BLAST of SMED30014876 vs. Planmine SMEST
Match: SMESG000025004.1 (SMESG000025004.1)

HSP 1 Score: 262.692 bits (670), Expect = 1.352e-88
Identity = 135/137 (98.54%), Postives = 136/137 (99.27%), Query Frame = 1
Query:  301 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECGK 711
            MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDA+CQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAE GK
Sbjct:    1 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDASCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAELGK 137          

HSP 2 Score: 62.7734 bits (151), Expect = 1.333e-11
Identity = 38/110 (34.55%), Postives = 57/110 (51.82%), Query Frame = 1
Query:  376 ELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAEC 705
            EL K+ELS  C  E+  +     TA +K+D  C+  Y  +  +   +   ++  C N IDKMSK+C  E     D FS+ I  LD SCD+EY  +++    +   LL +C
Sbjct:  134 ELGKKELSRSCQNELNLIYSEFETAIEKVDEDCEDKYFKIKKEYKPDSGPVQSICTNIIDKMSKKCSDEMILEQDLFSEAIGNLDTSCDQEYERMIRYFNRKIAILLGKC 243          
BLAST of SMED30014876 vs. Planmine SMEST
Match: SMESG000025002.1 (SMESG000025002.1)

HSP 1 Score: 212.231 bits (539), Expect = 6.690e-69
Identity = 116/187 (62.03%), Postives = 132/187 (70.59%), Query Frame = 1
Query:  199 SIEIVHELRQTSLNISTGLL*IH**IQ--------------TTHCIFKMKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECGKSR 717
            SI+I+H   QTSL+ S  +   H  +               T + I  MK F II LAILFVSIECRY+ARRVEL KRELSAECSKEVEKLD  LNTA D ID TCQK YD++++K   ++LK+E  CG  +  M+KEC  E KKLD SFSKEIDKLD SCDEEYANLVKNMKAEK KLLAECGKSR
Sbjct:   51 SIQIIHRPYQTSLDNSAKVRMKHLNVFKHFNLFAIKRAISFTFYYIIIMKAFFIISLAILFVSIECRYKARRVELFKRELSAECSKEVEKLDNQLNTAGDTIDKTCQKGYDEIMVKYGADFLKLETACGFEVSAMTKECSGEWKKLDSSFSKEIDKLDSSCDEEYANLVKNMKAEKAKLLAECGKSR 237          
BLAST of SMED30014876 vs. Planmine SMEST
Match: SMESG000025001.1 (SMESG000025001.1)

HSP 1 Score: 121.709 bits (304), Expect = 9.941e-35
Identity = 69/136 (50.74%), Postives = 88/136 (64.71%), Query Frame = 1
Query:  301 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECG 708
            M   LI   A+LFVSIECRY+  + EL+KRELS  C KE++K++E  + A  KID+ C  A+  +    S  YL +E  CG   DKMS+EC  E KKLDD F+KEI+KLD SCD E+A  V+N+  EK KL  EC 
Sbjct:    1 MNKLLIFAFALLFVSIECRYKLVQ-ELSKRELSESCQKELDKMNEDYDKAVAKIDSDCDAAFLKIEKPFSPLYLDVESRCGLDYDKMSEECIDETKKLDDDFTKEIEKLDSSCDAEFAKTVENLSKEKAKLKKECA 135          
The following BLAST results are available for this feature:
BLAST of SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 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 SMED30014876 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000054780.16.359e-94100.00SMESG000054780.1[more]
SMESG000025014.16.359e-94100.00SMESG000025014.1[more]
SMESG000025004.11.352e-8898.54SMESG000025004.1[more]
SMESG000025002.16.690e-6962.03SMESG000025002.1[more]
SMESG000025001.19.941e-3550.74SMESG000025001.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014876 ID=SMED30014876|Name=SMED30014876|organism=Schmidtea mediterranea sexual|type=transcript|length=737bp
CAGGTCCAAACATTCTTGTGCGTTTAATGAGAACTTGGAATAAAGTATTG
TAATTATTCATGGAGTGTATCAATCATTTTGGCACGTTTCAACTGGTCTG
CTAAAATGCATTAGCTCACTAGAATATACATGAATAGACATCTCTTGGTC
CTTCATCAATTCAAAAACAGCAAAATGAGCATCAATGGATCCGAATGAAG
CATTGAAATTGTTCATGAACTGCGTCAAACAAGTTTAAACATTTCAACTG
GTCTGCTATAAATACATTAATAAATACAAACAACTCATTGTATTTTCAAG
ATGAAAACCTTTCTTATTATTTGCTTGGCTATTTTATTCGTCTCTATCGA
ATGTCGTTATAGAGCTCGACGAGTTGAATTAAACAAGCGTGAATTGAGTG
CTGAATGCAGTAAAGAAGTCGAAAAATTGGACGAGGCGCTAAACACGGCT
ACTGACAAAATTGATGCAACTTGTCAGAAAGCATATGACGATCTTGTTAT
GAAAAACTCTGTAGAATATCTGAAAATCGAGAAAGATTGTGGTAATTACA
TAGATAAAATGTCGAAGGAATGTTATGCTGAAGCGAAAAAGTTAGATGAT
AGTTTTTCAAAGGAAATAGATAAATTGGATCAGTCTTGTGATGAAGAATA
TGCAAATCTTGTCAAAAACATGAAAGCAGAAAAAGTGAAATTGTTGGCTG
AATGTGGAAAGTCTCGTTGAGAAGTTTAATTAAAAAT
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protein sequence of SMED30014876-orf-1

>SMED30014876-orf-1 ID=SMED30014876-orf-1|Name=SMED30014876-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=140bp
MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTA
TDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDD
SFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAECGKSR*
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Aliases
The feature 'SMED30014876' has the following synonyms
Synonym
prog2-3
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0002032epidermal cell
PLANA:0002075pigment cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 29..53
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.72