SMED30016597

Overview
NameSMED30016597
Smed IDSMED30016597
Length (bp)743
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 SMED30016597 (SMED30016597) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016597 (SMED30016597) 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 SMED30016597 (SMED30016597) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016597 (SMED30016597) 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.
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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



SMED30016597

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
protonephridiaSMED30016597h1SMcG0011548 dd_Smed_v4_2607_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30016597h1SMcG0011548 dd_Smed_v4_2607_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
SMED30016597 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005813:3610..4354 +3619
Homology
[Close]
BLAST of SMED30016597 vs. Ensembl Fly
Match: CG42380 (gene:FBgn0259726 transcript:FBtr0299992)

HSP 1 Score: 48.1358 bits (113), Expect = 1.309e-7
Identity = 22/64 (34.38%), Postives = 35/64 (54.69%), Query Frame = -3 
Query:  517 QSINKARERLSKYSKLYLSCAPDGLTYAKCISTKKDLKQNICGAEFDAFKWCLKQNAEKMGTKI 708
            +S+ KA +R+  Y  L   CA     YA C+S   +++  IC  EF  F  C+++ A +M TK+
Sbjct:    2 ESVRKANQRIRNYPVLLSKCADKATAYAVCVSRDLNVQHKICDTEFKEFLSCIRKTALEMKTKL 65
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BLAST of SMED30016597 vs. Ensembl Fly
Match: CG42380 (gene:FBgn0259726 transcript:FBtr0299993)

HSP 1 Score: 48.1358 bits (113), Expect = 1.309e-7
Identity = 22/64 (34.38%), Postives = 35/64 (54.69%), Query Frame = -3 
Query:  517 QSINKARERLSKYSKLYLSCAPDGLTYAKCISTKKDLKQNICGAEFDAFKWCLKQNAEKMGTKI 708
            +S+ KA +R+  Y  L   CA     YA C+S   +++  IC  EF  F  C+++ A +M TK+
Sbjct:    2 ESVRKANQRIRNYPVLLSKCADKATAYAVCVSRDLNVQHKICDTEFKEFLSCIRKTALEMKTKL 65
[Close]
BLAST of SMED30016597 vs. TrEMBL
Match: A0A553PGX3 (Uncharacterized protein OS=Tigriopus californicus OX=6832 GN=TCAL_14709 PE=4 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 2.749e-9
Identity = 29/64 (45.31%), Postives = 43/64 (67.19%), Query Frame = -3 
Query:  517 SINKARERLSKYSKLYLSCAPDGLTYAKCISTK-KDLKQNICGAEFDAFKWCLKQNAEKMGTKI 705
            S+ KA+ RL  YSK   SC P+G  YAKC++    ++++  C AEFDAFK C++  A+K G+K+
Sbjct:    3 SVRKAKARLGSYSKWIASCGPEGAAYAKCVAQDLAEVQKGQCQAEFDAFKKCVQTAAKKAGSKL 66
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BLAST of SMED30016597 vs. TrEMBL
Match: A0A1W4WJV2 (uncharacterized protein C17orf89 homolog OS=Agrilus planipennis OX=224129 GN=LOC108736319 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 6.777e-8
Identity = 27/64 (42.19%), Postives = 39/64 (60.94%), Query Frame = -3 
Query:  517 QSINKARERLSKYSKLYLSCAPDGLTYAKCISTKKDLKQNICGAEFDAFKWCLKQNAEKMGTKI 708
            +S+ KA+ R  KY  L  +C  +   YAKC+  K  +K N C  EF+ FK CL+++A  MGT+I
Sbjct:    3 ESVKKAKSRFRKYPALLAACKSEASVYAKCVVNKDLIKVNNCAEEFNLFKKCLQKSAASMGTRI 66
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BLAST of SMED30016597 vs. TrEMBL
Match: E9GSJ9 (Uncharacterized protein OS=Daphnia pulex OX=6669 GN=DAPPUDRAFT_321320 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 1.301e-6
Identity = 26/69 (37.68%), Postives = 44/69 (63.77%), Query Frame = -3 
Query:  517 LIMNSQSINKARERLSKYSKLYLSCAPDGLTYAKCISTKKDLKQNICGAEFDAFKWCLKQNAEKMGTKI 723
            LIM+S  + KA+ RL  + +L   C    ++YAKC+  +++LKQN C  EF+  + C+ + A K+GT++
Sbjct:   79 LIMDS--VRKAQTRLKVFPQLLADCGGPAISYAKCVVVQENLKQNACLQEFNELRKCIHKAARKIGTRV 145
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BLAST of SMED30016597 vs. TrEMBL
Match: A0A2J7R9B6 (Uncharacterized protein OS=Cryptotermes secundus OX=105785 GN=B7P43_G16022 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 1.660e-6
Identity = 24/66 (36.36%), Postives = 40/66 (60.61%), Query Frame = -3 
Query:  517 NSQSINKARERLSKYSKLYLSCAPDGLTYAKCISTKKDLKQNICGAEFDAFKWCLKQNAEKMGTKI 714
             + S  KAR+RL +Y +L + C+     YA C+  K+++KQ  C  EF   + CL++ A +MGT++
Sbjct:   96 ETPSQTKARQRLRRYPELLIECSAPAAAYATCVLAKENVKQAECDREFQELRQCLQRAARRMGTRL 161
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BLAST of SMED30016597 vs. TrEMBL
Match: A0A2P8Y7V2 (GPI mannosyltransferase 1 OS=Blattella germanica OX=6973 GN=pigm PE=3 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.693e-6
Identity = 24/64 (37.50%), Postives = 42/64 (65.62%), Query Frame = -3 
Query:  517 QSINKARERLSKYSKLYLSCAPDGLTYAKCISTKKDLKQNICGAEFDAFKWCLKQNAEKMGTKI 708
            +S+ KAR+RL +Y ++ + C+     YA C+  K+++KQ  C  EF  F+ CL++ A +MGT++
Sbjct:    2 ESVLKARQRLRRYPEILVECSAPAAAYATCVLAKENVKQLECEREFQEFRHCLQKAAHRMGTRL 65
[Close]
BLAST of SMED30016597 vs. Planmine SMEST
Match: SMESG000063165.1 (SMESG000063165.1)

HSP 1 Score: 292.352 bits (747), Expect = 1.272e-97
Identity = 144/148 (97.30%), Postives = 145/148 (97.97%), Query Frame = 3 
Query:   21 FKKFQFTLSLIRPDKLNRINSGYEYAISDLTNNPFIHSSGIIIIPANAESRSLITYLDRNLIQQINSTKTEHNNNVSLFKRLKNVFISDFNCKEVILNVSIVNGITALKKLLSQLRSNYLTLNFDNCDLIIDQYYGTTTDGDVIIPWN 464
             KK QFTLSLIRPDK NRINSGYEYAISDLTNNPFIHSSGIIIIPANAESRSLITYLDRNLIQQINSTKTEHNNNVSLFKRLKNVFI+DFNCKEVILNVSIVNGITALKKLLSQLRSNYLTLNFDNCDLIIDQYYGTTTDGDVIIPWN
Sbjct:  285 LKKIQFTLSLIRPDKFNRINSGYEYAISDLTNNPFIHSSGIIIIPANAESRSLITYLDRNLIQQINSTKTEHNNNVSLFKRLKNVFITDFNCKEVILNVSIVNGITALKKLLSQLRSNYLTLNFDNCDLIIDQYYGTTTDGDVIIPWN 432
The following BLAST results are available for this feature:
BLAST of SMED30016597 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 SMED30016597 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 SMED30016597 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 2
Match NameE-valueIdentityDescription
CG423801.309e-734.38gene:FBgn0259726 transcript:FBtr0299992[more]
CG423801.309e-734.38gene:FBgn0259726 transcript:FBtr0299993[more]
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BLAST of SMED30016597 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 SMED30016597 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 SMED30016597 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 SMED30016597 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 SMED30016597 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A553PGX32.749e-945.31Uncharacterized protein OS=Tigriopus californicus ... [more]
A0A1W4WJV26.777e-842.19uncharacterized protein C17orf89 homolog OS=Agrilu... [more]
E9GSJ91.301e-637.68Uncharacterized protein OS=Daphnia pulex OX=6669 G... [more]
A0A2J7R9B61.660e-636.36Uncharacterized protein OS=Cryptotermes secundus O... [more]
A0A2P8Y7V21.693e-637.50GPI mannosyltransferase 1 OS=Blattella germanica O... [more]
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BLAST of SMED30016597 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 SMED30016597 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 SMED30016597 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 SMED30016597 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 SMED30016597 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 SMED30016597 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000063165.11.272e-9797.30SMESG000063165.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016597 ID=SMED30016597|Name=SMED30016597|organism=Schmidtea mediterranea sexual|type=transcript|length=743bp
GCTAGTGAATACATACGAAGTTTAAAAAATTTCAATTCACACTTTCATTA
ATTCGTCCAGATAAATTAAACAGAATAAATTCTGGTTATGAATACGCCAT
CAGTGATCTAACAAATAACCCCTTCATTCATTCTTCCGGAATAATTATTA
TTCCAGCTAATGCTGAATCAAGATCATTAATAACCTATCTAGACAGGAAC
TTAATTCAACAAATAAATTCAACCAAAACAGAACATAATAACAATGTATC
TTTATTTAAAAGATTGAAAAATGTTTTTATCTCAGACTTCAACTGCAAAG
AAGTTATTTTAAATGTTTCAATAGTTAATGGCATAACAGCTTTGAAAAAA
CTTCTTAGTCAATTAAGATCCAACTATTTAACTTTAAATTTTGATAATTG
TGACTTAATAATTGATCAATATTATGGAACAACCACAGATGGAGATGTTA
TTATTCCATGGAATTTTATTTGATATAATAAAATAAAAACATTTTATATT
TATTAAATTACAATCAAATTTTTGTACCCATTTTTTCGGCATTTTGCTTT
AAACACCACTTAAACGCATCAAATTCTGCACCACAAATGTTTTGTTTTAA
ATCTTTTTTAGTGGAAATACATTTGGCATAAGTCAAACCATCAGGTGCGC
AAGACAAATATAATTTGGAATATTTTGATAAACGTTCTCTAGCTTTATTA
ATAGATTGGGAATTCATAATTAAAAGGTCATTAAAAATGTTTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
Vocabulary: INTERPRO
TermDefinition
IPR034595NDUFAF8
IPR027989DUF4461
Vocabulary: cellular component
TermDefinition
GO:0005739mitochondrion
Vocabulary: biological process
TermDefinition
GO:0032981mitochondrial respiratory chain complex I assembly
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR034595NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 8PANTHERPTHR34561FAMILY NOT NAMEDcoord: 13..74