SMED30018142

Overview
NameSMED30018142
Smed IDSMED30018142
Length (bp)1850
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 SMED30018142 (SMED30018142) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018142 (SMED30018142) 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 SMED30018142 (SMED30018142) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018142 (SMED30018142) 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




SMED30018142

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30018142h1SMcG0021794 Contig51932newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018142h1SMcG0021794 Contig51932uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30018142h1SMcG0021794 dd_Smed_v4_9784_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30018142h1SMcG0021794 dd_Smed_v4_9784_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018142h1SMcG0021794 dd_Smed_v4_9784_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30018142h1SMcG0021794 dd_Smed_v4_9784_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30018142h1SMcG0021794 dd_Smed_v4_9784_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30018142h1SMcG0021794 dd_Smed_v4_9784_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30018142h1SMcG0021794 dd_Smed_v6_9784_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
secretory systemSMED30018142h1SMcG0021794 dd_Smed_v6_9784_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30018142 vs. Planmine SMEST
Match: SMESG000081436.1 (SMESG000081436.1)

HSP 1 Score: 450.669 bits (1158), Expect = 7.672e-140
Identity = 271/272 (99.63%), Postives = 271/272 (99.63%), Query Frame = 1
Query:   88 MINNFDDSVDEIYLKDQLIHELKGIIHEYENRLSAKDTNFQLQFSELQNELIGKESELDKINIXXXXXXXXXXXXXXXXXXXXXIIKSKDTALQIIQDDLKNQLENVKSHYNETLSIRQEEIESLRLTGSQLREQLALREDDMIQVMQRHENQIINMFNEIETKTEQSDVDQMVKILKDQIANLREALIDKQQSLKIANDKLEAQDQIMRKLQETNLDLEEQVKRYEQKYYTDQTYQKHIETLNDTLKENXXXXXXXXXXXXSLEKQLASLK 903
            MINNFDDSVDEIYLKDQLIHELKGIIHEYENRLSAKDTNFQLQFSELQNELIGKESELDKINIEKQKLECELLELHDLVDEHNLIIKSKDTALQIIQDDLKNQLENVKSHYNETLSIRQEEIESLRLTGSQLREQLAL EDDMIQVMQRHENQIINMFNEIETKTEQSDVDQMVKILKDQIANLREALIDKQQSLKIANDKLEAQDQIMRKLQETNLDLEEQVKRYEQKYYTDQTYQKHIETLNDTLKENKKKQLTFKAKAKSLEKQLASLK
Sbjct:    1 MINNFDDSVDEIYLKDQLIHELKGIIHEYENRLSAKDTNFQLQFSELQNELIGKESELDKINIEKQKLECELLELHDLVDEHNLIIKSKDTALQIIQDDLKNQLENVKSHYNETLSIRQEEIESLRLTGSQLREQLALLEDDMIQVMQRHENQIINMFNEIETKTEQSDVDQMVKILKDQIANLREALIDKQQSLKIANDKLEAQDQIMRKLQETNLDLEEQVKRYEQKYYTDQTYQKHIETLNDTLKENKKKQLTFKAKAKSLEKQLASLK 272          

HSP 2 Score: 384.415 bits (986), Expect = 6.394e-117
Identity = 229/230 (99.57%), Postives = 230/230 (100.00%), Query Frame = 1
Query:  901 KIEQMTCALQRLQLTQKSQIFTEHNIIDGNPVNSKYXXXXXXXXXXXXXXXFXXXXXXXXXXXXXXXXXXXXRLFLATDQLIHFRAFYADPDFKLKSEYLNPNKNISPKWSSFNNEIEDGHHQPHIKVLVXXXXXXXXXXXXXLMVSHAGSTVIKVEKSDRIRTPSSKTLFTRICGQMRNKKILNNIKSAMSADRGSLFFFRSQPRFNFKTLLTLYIMLIHVLLFHCMSS 1590
            +IEQMTCALQRLQLTQKSQIFTEHNIIDGNPVNSKYNNNLSESNSHEECENFLTELSELLEKKQSEIEELKSRLFLATDQLIHFRAFYADPDFKLKSEYLNPNKNISPKWSSFNNEIEDGHHQPHIKVLVESEDDQFSDSDDQLMVSHAGSTVIKVEKSDRIRTPSSKTLFTRICGQMRNKKILNNIKSAMSADRGSLFFFRSQPRFNFKTLLTLYIMLIHVLLFHCMSS
Sbjct: 3820 QIEQMTCALQRLQLTQKSQIFTEHNIIDGNPVNSKYNNNLSESNSHEECENFLTELSELLEKKQSEIEELKSRLFLATDQLIHFRAFYADPDFKLKSEYLNPNKNISPKWSSFNNEIEDGHHQPHIKVLVESEDDQFSDSDDQLMVSHAGSTVIKVEKSDRIRTPSSKTLFTRICGQMRNKKILNNIKSAMSADRGSLFFFRSQPRFNFKTLLTLYIMLIHVLLFHCMSS 4049          
BLAST of SMED30018142 vs. Planmine SMEST
Match: SMESG000081436.1 (SMESG000081436.1)

HSP 1 Score: 450.284 bits (1157), Expect = 9.301e-140
Identity = 271/272 (99.63%), Postives = 271/272 (99.63%), Query Frame = 1
Query:   88 MINNFDDSVDEIYLKDQLIHELKGIIHEYENRLSAKDTNFQLQFSELQNELIGKESELDKINIXXXXXXXXXXXXXXXXXXXXXIIKSKDTALQIIQDDLKNQLENVKSHYNETLSIRQEEIESLRLTGSQLREQLALREDDMIQVMQRHENQIINMFNEIETKTEQSDVDQMVKILKDQIANLREALIDKQQSLKIANDKLEAQDQIMRKLQETNLDLEEQVKRYEQKYYTDQTYQKHIETLNDTLKENXXXXXXXXXXXXSLEKQLASLK 903
            MINNFDDSVDEIYLKDQLIHELKGIIHEYENRLSAKDTNFQLQFSELQNELIGKESELDKINIEKQKLECELLELHDLVDEHNLIIKSKDTALQIIQDDLKNQLENVKSHYNETLSIRQEEIESLRLTGSQLREQLAL EDDMIQVMQRHENQIINMFNEIETKTEQSDVDQMVKILKDQIANLREALIDKQQSLKIANDKLEAQDQIMRKLQETNLDLEEQVKRYEQKYYTDQTYQKHIETLNDTLKENKKKQLTFKAKAKSLEKQLASLK
Sbjct:    1 MINNFDDSVDEIYLKDQLIHELKGIIHEYENRLSAKDTNFQLQFSELQNELIGKESELDKINIEKQKLECELLELHDLVDEHNLIIKSKDTALQIIQDDLKNQLENVKSHYNETLSIRQEEIESLRLTGSQLREQLALLEDDMIQVMQRHENQIINMFNEIETKTEQSDVDQMVKILKDQIANLREALIDKQQSLKIANDKLEAQDQIMRKLQETNLDLEEQVKRYEQKYYTDQTYQKHIETLNDTLKENKKKQLTFKAKAKSLEKQLASLK 272          

HSP 2 Score: 384.415 bits (986), Expect = 6.584e-117
Identity = 229/229 (100.00%), Postives = 229/229 (100.00%), Query Frame = 1
Query:  904 IEQMTCALQRLQLTQKSQIFTEHNIIDGNPVNSKYXXXXXXXXXXXXXXXFXXXXXXXXXXXXXXXXXXXXRLFLATDQLIHFRAFYADPDFKLKSEYLNPNKNISPKWSSFNNEIEDGHHQPHIKVLVXXXXXXXXXXXXXLMVSHAGSTVIKVEKSDRIRTPSSKTLFTRICGQMRNKKILNNIKSAMSADRGSLFFFRSQPRFNFKTLLTLYIMLIHVLLFHCMSS 1590
            IEQMTCALQRLQLTQKSQIFTEHNIIDGNPVNSKYNNNLSESNSHEECENFLTELSELLEKKQSEIEELKSRLFLATDQLIHFRAFYADPDFKLKSEYLNPNKNISPKWSSFNNEIEDGHHQPHIKVLVESEDDQFSDSDDQLMVSHAGSTVIKVEKSDRIRTPSSKTLFTRICGQMRNKKILNNIKSAMSADRGSLFFFRSQPRFNFKTLLTLYIMLIHVLLFHCMSS
Sbjct: 3838 IEQMTCALQRLQLTQKSQIFTEHNIIDGNPVNSKYNNNLSESNSHEECENFLTELSELLEKKQSEIEELKSRLFLATDQLIHFRAFYADPDFKLKSEYLNPNKNISPKWSSFNNEIEDGHHQPHIKVLVESEDDQFSDSDDQLMVSHAGSTVIKVEKSDRIRTPSSKTLFTRICGQMRNKKILNNIKSAMSADRGSLFFFRSQPRFNFKTLLTLYIMLIHVLLFHCMSS 4066          
The following BLAST results are available for this feature:
BLAST of SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 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 SMED30018142 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000081436.17.672e-14099.63SMESG000081436.1[more]
SMESG000081436.19.301e-14099.63SMESG000081436.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018142 ID=SMED30018142|Name=SMED30018142|organism=Schmidtea mediterranea sexual|type=transcript|length=1850bp
TATCAAACGTATCCATTCAAAAAATTATTATTGTCTAATTAATATATCAA
CAAAATACTTCAAATTAGAAGATTTTAATGATAAATTATGATCAATAATT
TTGATGATTCAGTTGACGAAATATATCTCAAAGATCAATTAATACATGAA
TTAAAAGGAATAATTCACGAATATGAAAATAGATTAAGCGCCAAAGATAC
AAATTTTCAACTACAATTTTCTGAATTACAAAATGAGTTAATCGGAAAAG
AATCAGAATTAGACAAAATTAATATCGAAAAGCAAAAATTAGAATGCGAA
TTACTTGAATTACACGATCTGGTTGATGAGCATAATTTAATAATTAAATC
TAAAGATACTGCGTTACAGATAATTCAAGATGATTTGAAAAATCAGTTAG
AAAATGTCAAAAGCCATTATAATGAAACATTGTCTATCCGCCAAGAAGAA
ATTGAGAGTTTGAGGTTGACTGGCAGTCAATTAAGAGAACAGTTAGCGTT
GCGAGAAGACGATATGATTCAAGTAATGCAAAGGCATGAAAATCAAATTA
TTAATATGTTCAATGAAATTGAAACAAAAACGGAACAATCTGATGTGGAT
CAAATGGTAAAGATCTTAAAAGACCAAATCGCAAATTTACGGGAAGCATT
AATTGATAAACAGCAATCACTAAAAATAGCAAATGACAAATTAGAAGCAC
AGGATCAGATCATGCGAAAACTGCAAGAAACAAATTTAGATTTAGAAGAA
CAAGTTAAACGTTACGAGCAAAAATATTACACTGATCAGACTTATCAAAA
ACATATTGAAACATTAAACGACACTTTAAAAGAAAATAAAAAGAAACAAT
TGACATTCAAAGCCAAAGCAAAATCGCTTGAAAAGCAACTAGCATCATTA
AAGATCGAACAAATGACGTGTGCACTTCAACGACTACAACTCACTCAGAA
ATCACAGATTTTCACAGAACATAATATCATTGATGGAAATCCAGTTAATT
CCAAATACAATAATAATTTGTCTGAATCAAATAGTCACGAAGAATGCGAA
AACTTTCTAACAGAATTATCTGAATTGTTAGAGAAAAAGCAAAGTGAAAT
AGAAGAATTGAAGAGTCGATTATTCTTAGCAACTGATCAATTAATACATT
TTCGTGCATTTTATGCTGATCCAGATTTTAAATTGAAATCGGAATATTTA
AATCCCAATAAAAATATAAGCCCTAAATGGAGTTCTTTCAACAATGAAAT
TGAGGATGGGCATCACCAACCGCATATCAAAGTTTTAGTCGAATCTGAAG
ACGATCAGTTTTCTGACAGTGATGACCAATTAATGGTTTCTCATGCTGGA
AGTACTGTTATTAAAGTGGAAAAATCAGATCGTATTCGGACCCCGTCCTC
AAAAACTCTCTTTACTCGAATATGTGGGCAAATGCGAAACAAGAAAATTT
TAAATAATATTAAATCTGCAATGTCAGCCGACAGAGGAAGTCTTTTCTTT
TTCAGGAGTCAACCCAGATTTAATTTCAAGACATTGTTGACGCTTTACAT
AATGCTAATTCATGTTTTATTATTTCATTGTATGTCCTCCTGACTCATTT
TCATCAAAAATCCTCTAAATGATAAATGATTATATTTTTTGTAGAATGGT
TAAAGGAATTATTACTGATTACTCTGCATTAAAAGCGACGAAATTGCAAA
ATGACACTGATTTAAACCCTTTTACTGCCTTTTATATTTAATTAATTTTA
AATATTTTATATTTGTTCAAACATTGAAGATGGTGCTACTCATAATTTAT
AATTTGTATATTATCACAAATCAACAGAAAATATAATTTTTTTTAAATTC
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protein sequence of SMED30018142-orf-1

>SMED30018142-orf-1 ID=SMED30018142-orf-1|Name=SMED30018142-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=502bp
MINNFDDSVDEIYLKDQLIHELKGIIHEYENRLSAKDTNFQLQFSELQNE
LIGKESELDKINIEKQKLECELLELHDLVDEHNLIIKSKDTALQIIQDDL
KNQLENVKSHYNETLSIRQEEIESLRLTGSQLREQLALREDDMIQVMQRH
ENQIINMFNEIETKTEQSDVDQMVKILKDQIANLREALIDKQQSLKIAND
KLEAQDQIMRKLQETNLDLEEQVKRYEQKYYTDQTYQKHIETLNDTLKEN
KKKQLTFKAKAKSLEKQLASLKIEQMTCALQRLQLTQKSQIFTEHNIIDG
NPVNSKYNNNLSESNSHEECENFLTELSELLEKKQSEIEELKSRLFLATD
QLIHFRAFYADPDFKLKSEYLNPNKNISPKWSSFNNEIEDGHHQPHIKVL
VESEDDQFSDSDDQLMVSHAGSTVIKVEKSDRIRTPSSKTLFTRICGQMR
NKKILNNIKSAMSADRGSLFFFRSQPRFNFKTLLTLYIMLIHVLLFHCMS
S*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000484secretory system
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 44..78
NoneNo IPR availableCOILSCoilCoilcoord: 122..142
NoneNo IPR availableCOILSCoilCoilcoord: 320..351
NoneNo IPR availableCOILSCoilCoilcoord: 174..229
NoneNo IPR availableCOILSCoilCoilcoord: 147..167