SMED30015082

Overview
NameSMED30015082
Smed IDSMED30015082
Length (bp)682
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 SMED30015082 (SMED30015082) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015082 (SMED30015082) 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 SMED30015082 (SMED30015082) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015082 (SMED30015082) 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



SMED30015082

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30015082SMESG000046965.1 SmedASXL_008943SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30015082SMESG000046965.1 dd_Smed_v4_13791_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30015082SMESG000046965.1 dd_Smed_v4_13791_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30015082SMESG000046965.1 dd_Smed_v6_13791_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30015082 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.022356:8772..9452 +3357
v31.018182:12613..13293 +3348
v31.019039:11456..12073 -3054
Homology
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BLAST of SMED30015082 vs. TrEMBL
Match: K1RMT1 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10018354 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 6.231e-10
Identity = 31/72 (43.06%), Postives = 47/72 (65.28%), Query Frame = 3 
Query:  189 YNTSEDHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVVVNMENSA 404
            Y + +D  GA  YVVAV++++GLSIV++IAS +R+N  D  +  YLKE+  +R    R++I   V N+  SA
Sbjct:    5 YKSDDDDIGALYYVVAVVMIYGLSIVMMIASHIRRNNQDNQLRSYLKEMSLLRKNDRRERIFTQVANVSTSA 76
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BLAST of SMED30015082 vs. TrEMBL
Match: V3ZQT2 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_166990 PE=4 SV=1)

HSP 1 Score: 66.6254 bits (161), Expect = 7.735e-10
Identity = 29/67 (43.28%), Postives = 50/67 (74.63%), Query Frame = 3 
Query:  204 DHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVVVNMENSA 404
            D  GA  YVVAV++++GLSIV++IAS +RKN+ D ++ +YLKE+  +R    R+KI++ V ++ +++
Sbjct:   41 DESGALFYVVAVVMIYGLSIVMMIASHIRKNKQDSHLRIYLKEMAVLRKNDRREKIMEQVNSIASTS 107
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BLAST of SMED30015082 vs. TrEMBL
Match: A0A2C9KT45 (Uncharacterized protein OS=Biomphalaria glabrata OX=6526 GN=106059450 PE=4 SV=1)

HSP 1 Score: 65.855 bits (159), Expect = 2.938e-9
Identity = 32/68 (47.06%), Postives = 47/68 (69.12%), Query Frame = 3 
Query:  195 TSEDHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVVVNMEN 398
            TS+D  GA  YVVAVI ++GLSIV++IAS +RKN+ D  +  YLKE+  +R    R+K+L  + ++ N
Sbjct:   83 TSDDDIGALYYVVAVIFIYGLSIVMMIASHIRKNKQDSQLRTYLKEMANLRKSDRREKVLSKMNDLAN 150
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BLAST of SMED30015082 vs. TrEMBL
Match: A0A433TCA8 (Uncharacterized protein OS=Elysia chlorotica OX=188477 GN=EGW08_012972 PE=4 SV=1)

HSP 1 Score: 66.6254 bits (161), Expect = 3.135e-9
Identity = 36/93 (38.71%), Postives = 57/93 (61.29%), Query Frame = 3 
Query:  114 KFRLNLINDSYFIASYVNQNKFNNIYNTSEDHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVVVNM 392
            K R+ +  DS    ++V      N+ +T +D  GA  YVVAVI ++GLSIV++IAS +RKN+ D  +  YLKE+  +R    R+K+L  + ++
Sbjct:   44 KLRIRVRPDSVQNDTWVGI--IENVQSTDDDDIGALYYVVAVIFIYGLSIVMMIASHIRKNKQDSQLRTYLKEMSNLRKTERREKVLHKMTDL 134
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BLAST of SMED30015082 vs. TrEMBL
Match: A0A2T7NPG4 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_16308 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 6.956e-8
Identity = 33/92 (35.87%), Postives = 57/92 (61.96%), Query Frame = 3 
Query:  126 NLINDSYFIASYVNQNKFNNIYNTSEDHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVVVNMENS 401
            ++ ND++    Y+   +    YN ++D  GA  YV+AVI ++GLSIV++IAS +RKN+ D  +  YLKE+  +R    R+K++  +  + N+
Sbjct:   23 DMGNDTWL--GYIEDRRR---YNENDD-IGALYYVIAVIFIYGLSIVMMIASHIRKNKQDCQLRAYLKEMAILRKADRREKLMGRISTLANA 108
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BLAST of SMED30015082 vs. Planmine SMEST
Match: SMESG000046965.1 (SMESG000046965.1)

HSP 1 Score: 371.318 bits (952), Expect = 8.732e-133
Identity = 182/185 (98.38%), Postives = 182/185 (98.38%), Query Frame = 3 
Query:   66 MYNSKFPQEHRHKLPIKFRLNLINDSYFIASYVNQNKFNNIYNTSEDHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVVVNMENSADIMTGLEEEVKQIKKPSHKPSAPIINRFIAPFKGRKIFIRINHLLEEHDRNVSRKCSLAVPEIFVEDEDERN 620
            MYNSKF QEH HKLPIKFRLNLINDSYFIASYVNQNKFNNIYNTSEDHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVVVNMENSADIMTGLEEEVKQIKKPSHKPS PIINRFIAPFKGRKIFIRINHLLEEHDRNVSRKCSLAVPEIFVEDEDERN
Sbjct:    1 MYNSKFQQEHHHKLPIKFRLNLINDSYFIASYVNQNKFNNIYNTSEDHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVVVNMENSADIMTGLEEEVKQIKKPSHKPSTPIINRFIAPFKGRKIFIRINHLLEEHDRNVSRKCSLAVPEIFVEDEDERN 185
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BLAST of SMED30015082 vs. Planmine SMEST
Match: SMESG000039006.1 (SMESG000039006.1)

HSP 1 Score: 88.1965 bits (217), Expect = 2.997e-21
Identity = 39/60 (65.00%), Postives = 52/60 (86.67%), Query Frame = 3 
Query:  204 DHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVV 383
            D +GA +YV AVI +WGL I LLIAST+RKNR+DK +SLYLKEIQ++R+ SD+QKIL+++
Sbjct:   60 DPKGAGIYVSAVIFIWGLCIALLIASTIRKNRMDKTISLYLKEIQSIRHNSDKQKILRLM 119
The following BLAST results are available for this feature:
BLAST of SMED30015082 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 SMED30015082 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 SMED30015082 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 SMED30015082 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 SMED30015082 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 SMED30015082 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 SMED30015082 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 SMED30015082 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
K1RMT16.231e-1043.06Uncharacterized protein OS=Crassostrea gigas OX=29... [more]
V3ZQT27.735e-1043.28Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
A0A2C9KT452.938e-947.06Uncharacterized protein OS=Biomphalaria glabrata O... [more]
A0A433TCA83.135e-938.71Uncharacterized protein OS=Elysia chlorotica OX=18... [more]
A0A2T7NPG46.956e-835.87Uncharacterized protein OS=Pomacea canaliculata OX... [more]
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BLAST of SMED30015082 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 SMED30015082 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 SMED30015082 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 SMED30015082 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 SMED30015082 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 SMED30015082 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000046965.18.732e-13398.38SMESG000046965.1[more]
SMESG000039006.12.997e-2165.00SMESG000039006.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015082 ID=SMED30015082|Name=SMED30015082|organism=Schmidtea mediterranea sexual|type=transcript|length=682bp
CTTTACTCAAATATCGCTAAATATTTCTTTTTTTTTATTTCGATTTGAAT
GTGTTGGTAAAAGATATGTACAATTCTAAATTTCCGCAGGAACATCGCCA
TAAATTGCCAATAAAATTCCGATTAAATCTTATCAATGATTCCTATTTCA
TTGCGTCATATGTTAATCAGAACAAATTCAACAACATTTACAATACGTCA
GAAGATCACCAAGGCGCTTTTATGTACGTTGTCGCAGTGATTTTGCTGTG
GGGTCTTTCGATTGTTTTATTAATTGCTTCGACTGTTAGAAAGAATCGGT
TGGATAAAAATGTGTCACTCTATCTTAAAGAGATTCAAGCCGTTCGAAAT
AGGTCCGACAGACAGAAAATTCTCCAAGTTGTGGTCAATATGGAAAATAG
CGCAGACATCATGACTGGACTGGAGGAAGAAGTGAAACAAATTAAAAAGC
CATCCCATAAACCGTCAGCGCCAATTATTAATAGATTCATTGCTCCATTT
AAAGGCAGAAAGATCTTTATTCGAATTAATCATTTGCTAGAAGAACACGA
TCGAAACGTAAGTAGAAAATGTTCTTTGGCTGTTCCGGAAATCTTTGTTG
AAGATGAAGACGAAAGAAATTGAACAATAATTGTAGATATAAAGATTCAT
TGATACCAAGCATTGTTTTAATTATAAATCTG
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protein sequence of SMED30015082-orf-1

>SMED30015082-orf-1 ID=SMED30015082-orf-1|Name=SMED30015082-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=186bp
MYNSKFPQEHRHKLPIKFRLNLINDSYFIASYVNQNKFNNIYNTSEDHQG
AFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQ
KILQVVVNMENSADIMTGLEEEVKQIKKPSHKPSAPIINRFIAPFKGRKI
FIRINHLLEEHDRNVSRKCSLAVPEIFVEDEDERN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head