SMED30019159

Overview
NameSMED30019159
Smed IDSMED30019159
Length (bp)1183
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 SMED30019159 (SMED30019159) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30019159 (SMED30019159) 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 SMED30019159 (SMED30019159) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30019159 (SMED30019159) 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



SMED30019159

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30019159SMESG000009968.1 SmedASXL_001390SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30019159SMESG000009968.1 dd_Smed_v4_15164_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30019159SMESG000009968.1 dd_Smed_v6_15164_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30019159SMESG000009968.1 OX_Smed_1.0.16099ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30019159SMESG000009968.1 dd_Smed_v4_15164_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30019159SMESG000009968.1 dd_Smed_v4_15164_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30019159 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004178:19592..23092 +5807
Homology
[Close]
BLAST of SMED30019159 vs. TrEMBL
Match: G4LY18 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 GN=Smp_149710 PE=4 SV=1)

HSP 1 Score: 78.5666 bits (192), Expect = 3.615e-12
Identity = 92/304 (30.26%), Postives = 121/304 (39.80%), Query Frame = 1 
Query:  232 SEPLWIPDRSPLLSTTNHRSDYRGHFHKTKIPGPDCLRAESKKSKVSAYLSTLPLSPPEDFDQGSNGKY------------------------------WLAENFLSKEVKWRRGNNLQLSQEPFDAFSHYQYDYPPKKPDEKVSYFPKHIPLKTEEKFNSVSTYNSDY------LKTQHNKDDICFKLNKPIPQNILTWRRENNFQKFQE---IKRNNLPPLDINTTYRSQFQYKA--PPLPIFHKSCEDLSP---------------KKYEPFNCRSSYQADYNSSVFEERDLMDIRLSSTG 975
            S PLWI D +     +  RSDY      ++   P+ +RA S K KVSAY ST+      D+D G   K                               WL +++ SK   WRR + +  ++E F   S Y+  +PPK+ D      P HIPLKT EKF   S Y  +Y      +   H+K     KL  PI       R E+N     E         P L  NTTYR  FQ  A     P+    C  ++P               + Y   N R  YQ DY SS+ + R L D RL + G
Sbjct:   21 SRPLWIKDPNYFDLQSLTRSDYLWDPRTSRKTEPEGIRARSFKPKVSAYKSTI------DWDSGEKEKSISCVHTQLNPNKYQNHSYSLTSLLDQQPRDWLIDDYDSKHKGWRRTDQIVRNKESFTKNSLYREQFPPKEADHVQPVKPVHIPLKTSEKFTDKSIYTDEYIWRPIIIDYSHSKH---HKLRLPIEMIPSKPRDESNMISIGENVMSAPGTSPKLFKNTTYREDFQRHALTSKEPVM---CRKIAPAIKLSKVLKPPYEIQESYSTINSR--YQYDYASSI-KHRHLSD-RLPAAG 308
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BLAST of SMED30019159 vs. TrEMBL
Match: A0A183ACS1 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS4756 PE=4 SV=1)

HSP 1 Score: 75.8702 bits (185), Expect = 5.454e-11
Identity = 69/239 (28.87%), Postives = 101/239 (42.26%), Query Frame = 1 
Query:  211 PNVSSVSSEPLWIPDRSPLLSTTNHRSDYRGHFHKTKIPGPDCLRAESKKSKVSAYLSTLPLSPPEDFDQG---SNGKYWLA-ENFL---------------SKEVKWRRGNNLQLSQEPFDAFSHYQYDYPPKKPDEKVSYFPKHIPLKTEEKFNSVSTYNSDY-------------LKTQHNKDDICFKLNKPIPQNILTWRRENNFQKFQEIKRNNLPPLDINTTYRSQFQYKAPP 831
            P+   + S PLWI ++  +   +    D+ GHFH T+   P  LRA S K KVSAY STL L  P     G      KY  A E  L               +  ++WRR   ++ S  P +  + Y+  YP K P+       KHIPLKTE+ F + S Y +D+             L+  H+           +P  I+  + E N     E +R    P++  ++Y   +Q   PP
Sbjct:    7 PDTRYLISRPLWIAEQPHVQVRSLMHDDFPGHFHVTRREAPYGLRARSYKPKVSAYRSTLQLQTPYRATGGISDHETKYNTASEKILFDPAYKDCRTVDDRQANRIRWRRMGQIERSILPQENETLYRSHYPIKTPEPVQRVTMKHIPLKTEQGFANNSVYKTDFANVKVPCKCYPTPLQRIHSNSS---GRQSTVP--IVNAKLEGNLTSIHETERGTNSPVN-KSSYEIDYQKYLPP 239
[Close]
BLAST of SMED30019159 vs. TrEMBL
Match: A0A3Q0KPN4 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 1.220e-10
Identity = 74/237 (31.22%), Postives = 96/237 (40.51%), Query Frame = 1 
Query:  232 SEPLWIPDRSPLLSTTNHRSDYRGHFHKTKIPGPDCLRAESKKSKVSAYLSTLPLSPPEDFDQGSNGKY------------------------------WLAENFLSKEVKWRRGNNLQLSQEPFDAFSHYQYDYPPKKPDEKVSYFPKHIPLKTEEKFNSVSTYNSDY------LKTQHNKDDICFKLNKPIPQNILTWRRENNFQKFQE---IKRNNLPPLDINTTYRSQFQYKA 825
            S PLWI D +     +  RSDY      ++   P+ +RA S K KVSAY ST+      D+D G   K                               WL +++ SK   WRR + +  ++E F   S Y+  +PPK+ D      P HIPLKT EKF   S Y  +Y      +   H+K     KL  PI       R E+N     E         P L  NTTYR  FQ  A
Sbjct:   14 SRPLWIKDPNYFDLQSLTRSDYLWDPRTSRKTEPEGIRARSFKPKVSAYKSTI------DWDSGEKEKSISCVHTQLNPNKYQNHSYSLTSLLDQQPRDWLIDDYDSKHKGWRRTDQIVRNKESFTKNSLYREQFPPKEADHVQPVKPVHIPLKTSEKFTDKSIYTDEYIWRPIIIDYSHSKH---HKLRLPIEMIPSKPRDESNMISIGENVMSAPGTSPKLFKNTTYREDFQRHA 241
[Close]
BLAST of SMED30019159 vs. TrEMBL
Match: A0A504Z6R8 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_10725 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 1.471e-9
Identity = 50/168 (29.76%), Postives = 77/168 (45.83%), Query Frame = 1 
Query:  211 PNVSSVSSEPLWIPDRSPLLSTTNHRSDYRGHFHKTKIPGPDCLRAESKKSKVSAYLSTLPLSPP-------------------EDFDQGSNGKYWLAENFLSKEVKWRRGNNLQLSQEPFDAFSHYQYDYPPKKPDEKVSYFPKHIPLKTEEKFNSVSTYNSDYLKT 657
            P+   + S+PLWI ++  +   +  R+DY GH H T+   P  LRA+S K KVSAY STL L  P                   E      + +  L ++  + + KW     ++ + EP +  S Y+ D+  K  +       KH+PL +EE F   S Y +D+ K 
Sbjct:    4 PDTRFLVSQPLWIAEQPNVEMKSLMRADYPGHIHATRSEVPYGLRAKSYKPKVSAYRSTLQLRTPYRSTGLMRNLEPGYTIRPEELLFDSRHQRDRLVDDRQANQCKWLSRGQIKRNDEPMERSSLYRLDFASKTLEPVRRITIKHVPLHSEEPFTGTSMYMTDFNKV 171
[Close]
BLAST of SMED30019159 vs. TrEMBL
Match: A0A183LU94 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS7369 PE=4 SV=1)

HSP 1 Score: 70.0922 bits (170), Expect = 2.489e-9
Identity = 82/293 (27.99%), Postives = 118/293 (40.27%), Query Frame = 1 
Query:  232 SEPLWIPDRSPLLSTTNHRSDYRGHFHKTKIPGPDCLRAESKKSKVSAYLSTLPLSPPEDFDQGSNGKY------------------------------WLAENFLSKEVKWRRGNNLQLSQEPFDAFSHYQYDYPPKKPDEKVSYFPKHIPLKTEEKFNSVSTYNSDYL---------KTQHNKDDICFKLNKPIPQNILTWRRENNFQKFQEIKRNNLPPLDIN----TTYRSQFQYKA--PPLPIFHKSCEDLSP---------------KKYEPFNCRSSYQADYNSSV 930
            S+PLWI D +     ++ RSDY      ++   P+ +RA S K KVSAY ST+      ++D G   K                               WL +++ SK   WRR + +  ++E F   S Y+  +PPK+        P HIPLKT EKF   S Y  +Y+         + +H+K  +C     PI       R E+N     E    ++P  + N    TTYR  FQ  A     P+    C  ++P               + Y   N R  YQ DY SS+
Sbjct:   14 SQPLWIKDPNYFDLQSSTRSDYLWDPRTSRKTEPEGIRARSFKPKVSAYKSTI------NWDLGEKSKSISCVHTQVNPNKFQNHSYSLTSLLDQQPRDWLIDDYDSKHKGWRRTDQIIRNKESFTKNSLYREQFPPKEAVHVQPVKPVHIPLKTSEKFTDKSVYTDEYIWRPILIDYNQLKHHK--LCL----PIEMIPSKPRDESNMINVGE-NVMSMPGTNPNLFKSTTYREDFQRHALTSKEPVM---CRKIAPVIKLSKILKPPYEIQESYSTINSR--YQYDYGSSI 288
[Close]
BLAST of SMED30019159 vs. Planmine SMEST
Match: SMESG000009968.1 (SMESG000009968.1)

HSP 1 Score: 593.964 bits (1530), Expect = 0.000e+0
Identity = 288/289 (99.65%), Postives = 288/289 (99.65%), Query Frame = 1 
Query:  196 MITKLPNVSSVSSEPLWIPDRSPLLSTTNHRSDYRGHFHKTKIPGPDCLRAESKKSKVSAYLSTLPLSPPEDFDQGSNGKYWLAENFLSKEVKWRRGNNLQLSQEPFDAFSHYQYDYPPKKPDEKVSYFPKHIPLKTEEKFNSVSTYNSDYLKTQHNKDDICFKLNKPIPQNILTWRRENNFQKFQEIKRNNLPPLDINTTYRSQFQYKAPPLPIFHKSCEDLSPKKYEPFNCRSSYQADYNSSVFEERDLMDIRLSSTGTLNKDTINNEFTLTPYLEYQRPVFHTVKQ 1062
            MITKLPNVSSVSSEPLWIPDRSPLLSTTNHRSDYRGHFHKTKIPGPDCLRAESKKSKVSAYLSTLPLSPPEDFDQGSNGKYWLAENFLSKEVKWRRGNNLQLSQEPFDA SHYQYDYPPKKPDEKVSYFPKHIPLKTEEKFNSVSTYNSDYLKTQHNKDDICFKLNKPIPQNILTWRRENNFQKFQEIKRNNLPPLDINTTYRSQFQYKAPPLPIFHKSCEDLSPKKYEPFNCRSSYQADYNSSVFEERDLMDIRLSSTGTLNKDTINNEFTLTPYLEYQRPVFHTVKQ
Sbjct:    1 MITKLPNVSSVSSEPLWIPDRSPLLSTTNHRSDYRGHFHKTKIPGPDCLRAESKKSKVSAYLSTLPLSPPEDFDQGSNGKYWLAENFLSKEVKWRRGNNLQLSQEPFDALSHYQYDYPPKKPDEKVSYFPKHIPLKTEEKFNSVSTYNSDYLKTQHNKDDICFKLNKPIPQNILTWRRENNFQKFQEIKRNNLPPLDINTTYRSQFQYKAPPLPIFHKSCEDLSPKKYEPFNCRSSYQADYNSSVFEERDLMDIRLSSTGTLNKDTINNEFTLTPYLEYQRPVFHTVKQ 289
The following BLAST results are available for this feature:
BLAST of SMED30019159 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 SMED30019159 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 SMED30019159 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 SMED30019159 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 SMED30019159 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 SMED30019159 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 SMED30019159 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 SMED30019159 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
G4LY183.615e-1230.26Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A183ACS15.454e-1128.87Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A3Q0KPN41.220e-1031.22Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A504Z6R81.471e-929.76Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
A0A183LU942.489e-927.99Uncharacterized protein OS=Schistosoma margrebowie... [more]
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BLAST of SMED30019159 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 SMED30019159 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 SMED30019159 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 SMED30019159 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 SMED30019159 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 SMED30019159 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000009968.10.000e+099.65SMESG000009968.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019159 ID=SMED30019159|Name=SMED30019159|organism=Schmidtea mediterranea sexual|type=transcript|length=1183bp
CTTCACTCCGATCAACAATCCATTGTTTTATCTTGCAATTGTAAATTTAA
CTCACTTTTCTTTTTCTATTTCCTCGCTTAAATTTGCAGTTTTCCATTGT
CTGTGGATATATTTTTATTCGACCAAGAATTCTACTTCAAGATCTTCAGG
CATTACTTCAGGTTTCTCAAGGTAGGTTTAAAACGGATTGCAAAAATGAT
TACAAAATTACCGAATGTCAGTTCGGTTTCTTCTGAACCGTTGTGGATTC
CTGACAGATCTCCATTGTTGTCGACGACAAATCACCGTTCCGATTACAGA
GGACATTTCCACAAAACAAAAATTCCCGGACCAGACTGTCTGAGAGCAGA
AAGTAAAAAGTCAAAAGTTTCAGCATATCTTTCTACTTTACCGTTGTCTC
CACCAGAGGATTTTGACCAAGGTTCAAACGGAAAATATTGGTTAGCAGAA
AATTTTCTTTCCAAAGAAGTTAAATGGAGAAGAGGAAATAATTTACAATT
GTCCCAAGAACCGTTTGATGCTTTTTCACATTATCAATACGATTATCCCC
CTAAAAAACCGGATGAAAAGGTGAGCTATTTCCCCAAGCACATTCCTTTG
AAGACAGAAGAAAAGTTTAACTCAGTCTCAACGTACAACAGTGATTATTT
GAAAACTCAACACAATAAAGATGATATTTGTTTCAAATTGAACAAACCGA
TCCCGCAAAATATTTTAACATGGAGACGGGAAAACAATTTCCAAAAGTTT
CAGGAAATCAAAAGAAACAATCTTCCTCCGTTGGACATCAATACTACTTA
TCGGTCCCAATTCCAATATAAGGCGCCTCCTTTACCAATATTTCACAAAA
GTTGTGAAGATCTTTCACCAAAGAAATACGAGCCCTTTAATTGCAGATCT
AGTTACCAAGCCGATTATAATTCTTCAGTGTTTGAAGAGAGAGATCTTAT
GGATATCCGACTTTCCAGTACTGGAACTCTCAATAAGGACACAATTAATA
ATGAATTTACCCTGACCCCTTACTTAGAATATCAAAGGCCAGTTTTTCAT
ACAGTAAAGCAATGAATGTACAGACTAGAATTGATATTAATATTATTTTC
ATTATTAGTTTATGATCCCAGATGTTCAACTTTTATATTGTAACCCTTTC
GTTTGTTTGTTATTGTTAATTATTGTTCTCTTA
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protein sequence of SMED30019159-orf-1

>SMED30019159-orf-1 ID=SMED30019159-orf-1|Name=SMED30019159-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=290bp
MITKLPNVSSVSSEPLWIPDRSPLLSTTNHRSDYRGHFHKTKIPGPDCLR
AESKKSKVSAYLSTLPLSPPEDFDQGSNGKYWLAENFLSKEVKWRRGNNL
QLSQEPFDAFSHYQYDYPPKKPDEKVSYFPKHIPLKTEEKFNSVSTYNSD
YLKTQHNKDDICFKLNKPIPQNILTWRRENNFQKFQEIKRNNLPPLDINT
TYRSQFQYKAPPLPIFHKSCEDLSPKKYEPFNCRSSYQADYNSSVFEERD
LMDIRLSSTGTLNKDTINNEFTLTPYLEYQRPVFHTVKQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000096ventral epidermis
PLANA:0000418head