SMED30007838

Overview
NameSMED30007838
Smed IDSMED30007838
Length (bp)458
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 SMED30007838 (SMED30007838) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007838 (SMED30007838) 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 SMED30007838 (SMED30007838) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007838 (SMED30007838) 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



SMED30007838

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30007838SMESG000017434.1 dd_Smed_v4_11003_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007838SMESG000017434.1 dd_Smed_v4_11003_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
SMED30007838 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000691:18569..19026 +2272
Homology
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BLAST of SMED30007838 vs. Ensembl Xenopus
Match: ENSXETT00000024080.1 (ribosomal biogenesis protein LAS1L-like [Source:NCBI gene;Acc:100495727])

HSP 1 Score: 48.9062 bits (115), Expect = 3.081e-7
Identity = 15/78 (19.23%), Postives = 46/78 (58.97%), Query Frame = 3 
Query:  213 AYAISKFITLTFQNMVKKNPDFCSKPMQDVLSEIGVPLYIISLRNEIVHGSCPAAQLLDLAFEDIIHWIKKNFWNKYL 446
              A+ +F+ L    + ++     + P++ + +E+G+P ++++LR+++ HG  P   +    ++ ++ W+++ +W++ L
Sbjct:   81 GLALVRFVNL----ITERKQKTVAIPLRRLANEVGIPEWVVNLRHDLTHGKLPKLSMCRKGWDCVMEWLRREYWSRQL 154
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BLAST of SMED30007838 vs. TrEMBL
Match: A0A2H1BST5 (Ribosomal L38e protein OS=Fasciola hepatica OX=6192 GN=D915_15188 PE=3 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 7.109e-8
Identity = 30/93 (32.26%), Postives = 52/93 (55.91%), Query Frame = 3 
Query:  165 TLNLISAYLDNSRYSMAYAISKFITLTFQNMVKKNPDFCSKPMQDVLSEIGVPLYIISLRNEIVHGSCPAAQLLDLAFEDIIHWIKK---NFW 434
            T +L+ AYL+NS  S+A A+ +F++L       ++  + + P+  +  + G+P +++ LRN++ HGS P+  LL   F    HW  K    FW
Sbjct:   57 TYHLLVAYLENSDQSLALALMRFVSLLSSEDQDRDRPYLAAPLLSLARQAGLPSWLVDLRNDVAHGSLPSPALLASGF----HWASKCLTEFW 145
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BLAST of SMED30007838 vs. TrEMBL
Match: A0A4E0QVB1 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_010757 PE=3 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 7.172e-8
Identity = 30/93 (32.26%), Postives = 52/93 (55.91%), Query Frame = 3 
Query:  165 TLNLISAYLDNSRYSMAYAISKFITLTFQNMVKKNPDFCSKPMQDVLSEIGVPLYIISLRNEIVHGSCPAAQLLDLAFEDIIHWIKK---NFW 434
            T +L+ AYL+NS  S+A A+ +F++L       ++  + + P+  +  + G+P +++ LRN++ HGS P+  LL   F    HW  K    FW
Sbjct:   57 TYHLLVAYLENSDQSLALALMRFVSLLSSEDQDRDRPYLAAPLLSLARQAGLPSWLVDLRNDVAHGSLPSPALLASGF----HWASKCLTEFW 145
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BLAST of SMED30007838 vs. TrEMBL
Match: A0A2B4SFC2 (Ribosomal biogenesis protein LAS1L OS=Stylophora pistillata OX=50429 GN=LAS1L PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 3.868e-7
Identity = 29/98 (29.59%), Postives = 53/98 (54.08%), Query Frame = 3 
Query:  156 VNQTLNLISAYLDNSRYSMAYAISKFITLTFQNMVKKNPDF-CSKPMQDVLSEIGVPLYIISLRNEIVHGSCPAAQLLDLAFEDIIHWIKKNFWNKYL 446
            V  T NLISA+LD  R ++A AI +F+      MV ++     ++ +Q +  EIG+P +++ +R+E  H + P+ + L       + W++  +W   L
Sbjct:   54 VESTANLISAHLDQGRLTLAMAIVRFVN----GMVDQDQKGKFARSVQTIGEEIGLPKWLVDIRHESAHQNLPSLETLRCGVRASLSWLQSEYWEAQL 147
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BLAST of SMED30007838 vs. TrEMBL
Match: A0A1W2WAK5 (uncharacterized protein LOC100183975 OS=Ciona intestinalis OX=7719 GN=LOC100183975 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 8.511e-7
Identity = 27/79 (34.18%), Postives = 47/79 (59.49%), Query Frame = 3 
Query:  201 RYSMAYAISKFITLTFQNMVKKNPDFCSKPMQDVLSEIGVPLYIISLRNEIVHGSCPAAQLLDLAFEDIIHWIKKNFWN 437
            R  M+ A+++F+ L  +  +K N     KP+  V  ++G+P ++I+LR+E+ HG  PA  +L  A    I W+K+N W+
Sbjct:   73 RQMMSAAVTQFVGLLTEKGLKGN---VRKPIHHVGVDLGIPEWLINLRHEMAHGPLPALPMLHKAVTFAIDWLKENHWD 148
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BLAST of SMED30007838 vs. TrEMBL
Match: A0A5J4N7V4 (Uncharacterized protein OS=Paragonimus westermani OX=34504 GN=DEA37_0002373 PE=4 SV=1)

HSP 1 Score: 55.4546 bits (132), Expect = 4.744e-6
Identity = 23/76 (30.26%), Postives = 44/76 (57.89%), Query Frame = 3 
Query:  171 NLISAYLDNSRYSMAYAISKFITLTFQNMVKKNPDFCSKPMQDVLSEIGVPLYIISLRNEIVHGSCPAAQLLDLAF 398
            NL+ AY ++S  S+A A+ +F++L   +   +   + ++ +  +   +G P ++  +RN+I HGS P A LL+  F
Sbjct:   59 NLLVAYFEHSHQSLALALMRFVSLVSSDEQDREKPYSARSLLALTRRVGFPCWLADMRNDIAHGSIPCACLLERGF 134
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BLAST of SMED30007838 vs. Planmine SMEST
Match: SMESG000017434.1 (SMESG000017434.1)

HSP 1 Score: 169.474 bits (428), Expect = 1.151e-55
Identity = 84/84 (100.00%), Postives = 84/84 (100.00%), Query Frame = 3 
Query:   48 MEAISYNLSNFIINNELVNHIKEVNNSNIDNDSKFYVNQTLNLISAYLDNSRYSMAYAISKFITLTFQNMVKKNPDFCSKPMQD 299
            MEAISYNLSNFIINNELVNHIKEVNNSNIDNDSKFYVNQTLNLISAYLDNSRYSMAYAISKFITLTFQNMVKKNPDFCSKPMQD
Sbjct:    1 MEAISYNLSNFIINNELVNHIKEVNNSNIDNDSKFYVNQTLNLISAYLDNSRYSMAYAISKFITLTFQNMVKKNPDFCSKPMQD 84
The following BLAST results are available for this feature:
BLAST of SMED30007838 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 SMED30007838 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 SMED30007838 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 SMED30007838 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 SMED30007838 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSXETT00000024080.13.081e-719.23ribosomal biogenesis protein LAS1L-like [Source:NC... [more]
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BLAST of SMED30007838 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 SMED30007838 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 SMED30007838 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2H1BST57.109e-832.26Ribosomal L38e protein OS=Fasciola hepatica OX=619... [more]
A0A4E0QVB17.172e-832.26Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A2B4SFC23.868e-729.59Ribosomal biogenesis protein LAS1L OS=Stylophora p... [more]
A0A1W2WAK58.511e-734.18uncharacterized protein LOC100183975 OS=Ciona inte... [more]
A0A5J4N7V44.744e-630.26Uncharacterized protein OS=Paragonimus westermani ... [more]
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BLAST of SMED30007838 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 SMED30007838 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 SMED30007838 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 SMED30007838 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 SMED30007838 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 SMED30007838 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000017434.11.151e-55100.00SMESG000017434.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007838 ID=SMED30007838|Name=SMED30007838|organism=Schmidtea mediterranea sexual|type=transcript|length=458bp
TGATTTTAATGAGATTAATTTGTTTGAATATTCAATAGTCTTTGTAAATG
GAAGCTATTTCTTATAATCTCAGCAACTTTATAATTAATAACGAACTAGT
TAATCATATAAAAGAAGTTAACAATTCCAATATTGATAATGATTCAAAAT
TTTATGTTAATCAGACATTAAATTTAATTTCAGCATATTTGGACAATAGC
AGATATTCAATGGCGTACGCTATTAGCAAATTCATTACATTAACCTTTCA
AAATATGGTAAAGAAAAATCCAGATTTCTGTTCAAAACCAATGCAAGATG
TATTATCAGAAATTGGTGTACCTCTTTATATCATTTCTCTTAGAAATGAA
ATTGTTCATGGATCTTGTCCTGCTGCTCAACTTCTTGATCTCGCTTTTGA
AGATATAATTCATTGGATTAAAAAAAATTTCTGGAATAAATATTTGTGAT
ACTTTTTC
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protein sequence of SMED30007838-orf-1

>SMED30007838-orf-1 ID=SMED30007838-orf-1|Name=SMED30007838-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=134bp
MEAISYNLSNFIINNELVNHIKEVNNSNIDNDSKFYVNQTLNLISAYLDN
SRYSMAYAISKFITLTFQNMVKKNPDFCSKPMQDVLSEIGVPLYIISLRN
EIVHGSCPAAQLLDLAFEDIIHWIKKNFWNKYL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
Vocabulary: molecular function
TermDefinition
GO:0004519endonuclease activity
Vocabulary: biological process
TermDefinition
GO:0006364rRNA processing
Vocabulary: cellular component
TermDefinition
GO:0090730Las1 complex
Vocabulary: INTERPRO
TermDefinition
IPR007174Las1
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007174Las1PFAMPF04031Las1coord: 47..130
e-value: 5.8E-13
score: 49.2