SMED30021628

Overview
NameSMED30021628
Smed IDSMED30021628
Length (bp)1336
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 SMED30021628 (SMED30021628) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021628 (SMED30021628) 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 SMED30021628 (SMED30021628) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021628 (SMED30021628) 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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Alignments
SMED30021628 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.019120:5522..7793 -5474
Homology
BLAST of SMED30021628 vs. TrEMBL
Match: A0A5K4F607 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 92.0485 bits (227), Expect = 2.131e-19
Identity = 43/53 (81.13%), Postives = 48/53 (90.57%), Query Frame = -2
Query:  673 LMESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK 831
            L++ GFVFK+GRLFKTPYGGEGVDF DQLNYQFT GL+VIFI I+S RQYVGK
Sbjct:    8 LLDGGFVFKLGRLFKTPYGGEGVDFIDQLNYQFTGGLMVIFIAIISFRQYVGK 60          
BLAST of SMED30021628 vs. TrEMBL
Match: A0A430QHZ8 (Uncharacterized protein OS=Schistosoma bovis OX=6184 GN=DC041_0007936 PE=4 SV=1)

HSP 1 Score: 92.0485 bits (227), Expect = 2.131e-19
Identity = 43/53 (81.13%), Postives = 48/53 (90.57%), Query Frame = -2
Query:  673 LMESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK 831
            L++ GFVFK+GRLFKTPYGGEGVDF DQLNYQFT GL+VIFI I+S RQYVGK
Sbjct:    8 LLDGGFVFKLGRLFKTPYGGEGVDFIDQLNYQFTGGLMVIFIAIISFRQYVGK 60          
BLAST of SMED30021628 vs. TrEMBL
Match: A0A183P566 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS9502 PE=4 SV=1)

HSP 1 Score: 92.0485 bits (227), Expect = 2.131e-19
Identity = 43/53 (81.13%), Postives = 48/53 (90.57%), Query Frame = -2
Query:  673 LMESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK 831
            L++ GFVFK+GRLFKTPYGGEGVDF DQLNYQFT GL+VIFI I+S RQYVGK
Sbjct:    8 LLDGGFVFKLGRLFKTPYGGEGVDFIDQLNYQFTGGLMVIFIAIISFRQYVGK 60          
BLAST of SMED30021628 vs. TrEMBL
Match: A0A2H1CXM3 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_00116 PE=4 SV=1)

HSP 1 Score: 91.2781 bits (225), Expect = 7.212e-19
Identity = 40/53 (75.47%), Postives = 49/53 (92.45%), Query Frame = -2
Query:  673 LMESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK 831
            L++ GFVFK+GRLF+TPYGGEGVDF DQLNYQFT GL++IFI I+S+RQYVG+
Sbjct:    8 LLDGGFVFKLGRLFRTPYGGEGVDFVDQLNYQFTGGLMIIFIAIISLRQYVGQ 60          
BLAST of SMED30021628 vs. TrEMBL
Match: A0A448XG29 (Uncharacterized protein OS=Protopolystoma xenopodis OX=117903 GN=PXEA_LOCUS29400 PE=4 SV=1)

HSP 1 Score: 93.5893 bits (231), Expect = 1.671e-18
Identity = 52/66 (78.79%), Postives = 57/66 (86.36%), Query Frame = -2
Query:  676 GF*KMARXXXXXXGLMESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVG 873
            G  KMARGAGG   L++ GFVFK+GRLFKTPYGGEGVDF DQLNYQFT GL+VIFI IVS+RQYVG
Sbjct:   53 GIFKMARGAGG---LLDGGFVFKLGRLFKTPYGGEGVDFVDQLNYQFTGGLMVIFIAIVSLRQYVG 115          
BLAST of SMED30021628 vs. Planmine SMEST
Match: SMESG000068735.1 (SMESG000068735.1)

HSP 1 Score: 113.62 bits (283), Expect = 1.812e-27
Identity = 63/63 (100.00%), Postives = 63/63 (100.00%), Query Frame = -2
Query:  673 MARXXXXXXGLMESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK 861
            MARGAGGGGGLMESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK
Sbjct:    1 MARGAGGGGGLMESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK 63          
BLAST of SMED30021628 vs. Planmine SMEST
Match: SMESG000075619.1 (SMESG000075619.1)

HSP 1 Score: 71.2478 bits (173), Expect = 1.162e-13
Identity = 29/51 (56.86%), Postives = 43/51 (84.31%), Query Frame = -2
Query:  676 MESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVG 828
            ME+G + K+G+LF T YGG  +DF DQ+NYQ++SGL++IFI+I+ +RQ+VG
Sbjct:    1 MENGAIIKLGKLFHTNYGGNDIDFVDQINYQYSSGLLLIFISIIGLRQFVG 51          
BLAST of SMED30021628 vs. Planmine SMEST
Match: SMESG000027007.1 (SMESG000027007.1)

HSP 1 Score: 72.4034 bits (176), Expect = 1.425e-13
Identity = 32/52 (61.54%), Postives = 38/52 (73.08%), Query Frame = -2
Query:  673 MESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK 828
            M +G   KI R FK PYGG  VDF DQLNYQFTSGL+ +F+ I+  RQY+GK
Sbjct:    1 MNAGIFLKIIRFFKVPYGGADVDFVDQLNYQFTSGLLAVFVIIIGFRQYMGK 52          
BLAST of SMED30021628 vs. Planmine SMEST
Match: SMESG000033444.1 (SMESG000033444.1)

HSP 1 Score: 70.8626 bits (172), Expect = 5.169e-13
Identity = 39/52 (75.00%), Postives = 46/52 (88.46%), Query Frame = -2
Query:  673 MESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK 828
            MESG  F+IG+LF+ PYGGEGVDF DQLNYQFTSGL+++FI I+ IRQYVGK
Sbjct:    1 MESGIFFRIGQLFRVPYGGEGVDFVDQLNYQFTSGLLIVFIIIIGIRQYVGK 52          
BLAST of SMED30021628 vs. Planmine SMEST
Match: SMESG000051126.1 (SMESG000051126.1)

HSP 1 Score: 68.9366 bits (167), Expect = 2.071e-12
Identity = 30/52 (57.69%), Postives = 39/52 (75.00%), Query Frame = -2
Query:  673 MESGFVFKIGRLFKTPYGGEGVDFADQLNYQFTSGLIVIFITIVSIRQYVGK 828
            ME+    KIG+ F T YGG  +DF DQLNYQ+++GL+ IFI+I+  RQYVGK
Sbjct:    1 METNTFLKIGKHFHTAYGGNDIDFVDQLNYQYSTGLLFIFISIIGFRQYVGK 52          
The following BLAST results are available for this feature:
BLAST of SMED30021628 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 SMED30021628 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 SMED30021628 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 SMED30021628 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 SMED30021628 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 SMED30021628 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 SMED30021628 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 SMED30021628 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A5K4F6072.131e-1981.13Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A430QHZ82.131e-1981.13Uncharacterized protein OS=Schistosoma bovis OX=61... [more]
A0A183P5662.131e-1981.13Uncharacterized protein OS=Schistosoma mattheei OX... [more]
A0A2H1CXM37.212e-1975.47Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A448XG291.671e-1878.79Uncharacterized protein OS=Protopolystoma xenopodi... [more]
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BLAST of SMED30021628 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 SMED30021628 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 SMED30021628 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 SMED30021628 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 SMED30021628 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 SMED30021628 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000068735.11.812e-27100.00SMESG000068735.1[more]
SMESG000075619.11.162e-1356.86SMESG000075619.1[more]
SMESG000027007.11.425e-1361.54SMESG000027007.1[more]
SMESG000033444.15.169e-1375.00SMESG000033444.1[more]
SMESG000051126.12.071e-1257.69SMESG000051126.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021628 ID=SMED30021628|Name=SMED30021628|organism=Schmidtea mediterranea sexual|type=transcript|length=1336bp
TTGTACGACTATTGTATATACAAATATAAAAACATTATTTTTGTATATAC
AATAGTCGTACAAAGTCAAAGAAAAGTTAATAAATGTATATTGGATTATT
TGCAGTTTTATGTGATCTACATTATTATCCCAAACCTTATTTCAAGAGTA
GTAAGCAATTATTTTTTTTCCGCCTTCTTTGATATCGTTTCTGTATTTTA
GTTAGAGACTAAGATAAAACTTCTCTCAATGTTACTTAGTAAAAACACAA
AGGATTTTTTTCAAAAAAATTAGGATACAAGAGCAAAAAGTGGAACTTGA
GTGCTATATTGCAATCTAAAATATATTAGCATTCATTGCAGTTTATTTTA
CAAAATTTGTCACTAGGAAATTAATATCAAAACTCTTGAATTCATTCCAT
AATGATATTTATAGCTATTTCATTTTGTTTTCTATAATTTATGATGCAAT
ATCTGTTTTAGCTGTGATTTGTCACCATTTGCCTAGATCAGTGTTGTGCA
ACTCAAAATACCACGGCACTTTNNANNNNNATTNNAANNTNNTTNAAGAA
ANNNANNTATNNNNAAATANNGNNATTTTACNANNANNANNNNNNNNANA
TTNAANNANNNGNTNGNTAAANTNAANCANTCATNNNTNNNANNAATANN
NNTNNANANTNNNANATGTTCACTTACCGACATATTGGCGAATACTGACA
ATAGTAATGAAAATAACAATCAATCCACTAGTAAACTGATAATTTAATTG
ATCTGCGAAGTCGACTCCTTCACCTCCATATGGAGTTTTAAAAAGTCGAC
CAATTTTGAATACAAATCCACTTTCCATTAATCCACCACCACCTCCGGCT
CCTCTTGCCATTTTTCAAAATCCAAAACAAACGAAAATTATTGGCAAAAT
ATCGAAAAATCCAGTTTGAATTGAATATTGTTCAAAGATTGGTTATTAGT
CAAATTTTGTGTCATTACAGTTTNNAANNTNTGNNNNGNTANAANANANA
NTANAATNNCNATNNNNCANAGNNGNANANTNANNGNATANTTNGANNNN
NANANTCANNNNANATATTNANNNNTAANNNGNAGNCACAAATCAATAAT
ATTCAATCTAACAAGGAGGGTACCAGTTGCAGTAGTGTTATTCAAAAAAA
ATTTCAAAATATGCAGCAGTGCAAGACAAGCAGCAAGCAAGATAATTCCA
TACCTAAACTGAGTAACGAAGGCTGAGTATGTGTTCGTTGAGGATGTATT
CAATTTTTTTTGTCTTTTCTAGAGAAATTGTATGTCTTATTTTATCATTT
TCAGAGGCGTGTCTGTGTTTGTGTGTTTTGGAGATC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR000990Innexin
Vocabulary: cellular component
TermDefinition
GO:0005921gap junction
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000990InnexinPFAMPF00876Innexincoord: 34..63
e-value: 1.8E-5
score: 24.2
NoneNo IPR availableTMHMMTMhelixcoord: 39..61