SMED30000132

Overview
NameSMED30000132
Smed IDSMED30000132
Length (bp)2726
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 SMED30000132 (SMED30000132) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000132 (SMED30000132) 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 SMED30000132 (SMED30000132) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30000132 (SMED30000132) 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



SMED30000132

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30000132SMESG000017239.1 dd_Smed_v4_4431_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30000132SMESG000017239.1 dd_Smed_v4_4431_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30000132SMESG000017239.1 dd_Smed_v4_4431_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30000132SMESG000017239.1 dd_Smed_v4_4431_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000132SMESG000017239.1 dd_Smed_v4_4431_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30000132SMESG000017239.1 dd_Smed_v4_4431_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30000132SMESG000017239.1 dd_Smed_v4_4431_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000132SMESG000017239.1 Contig21750uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000132SMESG000017239.1 Contig21750newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000132SMESG000017239.1 Contig38754newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000132SMESG000017239.1 Contig38754uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30000132SMESG000017239.1 dd_Smed_v4_4431_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
SMED30000132 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000932:10177..21862 +13092
Homology
[Close]
BLAST of SMED30000132 vs. Planmine SMEST
Match: SMESG000017239.1 (SMESG000017239.1)

HSP 1 Score: 1337.78 bits (3461), Expect = 0.000e+0
Identity = 717/724 (99.03%), Postives = 718/724 (99.17%), Query Frame = 1 
Query:  187 MEEAXXXXXXXXXXXXXXDQLTGMIQSNGINLVNDQNLNNMIVSLCQRFELKMKSKLTLGVIFDCKYNEPCLIDALLNEKVSPLLDSKYPYVIQGEESVKETRVDHSSKDIKMISVPNEKWKYFNNSVMLLSNNDFKDFLSQISLKSVFDPDVLVLVLKSADELQDPKIQSFISSIKNQNFDPTFLLVLNDAESIDCTAYDYCDVCYPENVRQYLQDAQMNLENRIFKISASKILRSGGDPQAMSAENEHLAKNFTDFKEVFQRDLDIDNVMDRFYRTAQVIGESMDELRKTFDENKLKEVITECETSLVKESSGVIEDIQNQKSNTLKDVKQIFDDRNNDENEFLRSILKKVMKQKCGNLRQDLEGXXXXXXXXXXXXNYNKEVSAMSRNIFTXXXXXXXXXXXXIDDFISNEIDEFKLMDIKKENMDFGKINVEEIDFDKLRNSANQKEKKQAKTVLYKFLYSWKTAIFKIYNVAENAYKIFTAAFXXXXXXXXXXXXXTIDFTVKFSKELHLRHMVKECRKMKQVIETKRKQIRDGIHLHVDLINDKLISIDNEDLKSEKMGNLLGDLMENFEKSCNMAALKHELYTQMQNTGSSELSQKITDHFADQYQKKYLTSAEVDKFDKQIKDQMGKLYKKIDEKKFYVHSKEDFFDIDNENPKTLEELNVMKKEKRSIKTSELMMQLHSTTNDMVTLLNETSNKLNEGIDKFILYMKNYSFEVAV 2358
            MEEAKSYEEKFEKIKEIYDQLTGMIQSNGINLVNDQNLNNMIVSLCQRFELKMKSKLTLGVIFDCKYNEPCLIDALLNEKVSPLLDSKYPYVIQGEESVKETRVDHSSKDIKMISVPNEKWK FNNSVMLLSNNDFKDFLSQISLKSVFDPDVLVLVLKSADELQDPKIQSFISSIKNQNFDPTFLLVLNDAESIDCT YDYCDVCYPENVRQYLQDAQMNLENRIFKISASKILRSGGDPQAMSAENEHLAKNFTDFKEVFQRDLDIDNVMDRFYRTAQVIGESMDELRKTFDENKLKEVITECETSLVKESSGVIEDIQNQKSNTLKDV QI DDRNNDENEFLRSILKKVMKQKCGNLRQDLEGKITKIIQKIKDKNYNKEVS MSRNIFTKEYLNEEKLENNIDDFISNEIDEFKLMDIKKENMDFGKINVEEIDFDKLRNSANQKEKKQAKTVLYKFLYSWKTAIFKIYNVAENAYK FTAAFKKKVVNVVEDVKKTIDFTVKFSKELHLRHMVKECRKMKQVIETKRKQIRDGIHLHVDLINDKLISIDNEDLKSEKMGNLLGDLMENFEKSCNMAALKHELYTQMQNTGSSELSQKITDHFADQYQKKYLTSAEVDKFDKQIKDQMGKLYKKIDEKKFYVHSKEDFFDIDNENPKTLEELNVM+KEKRSIKTSELMMQLHSTTNDMVTLLNETSNKLNEGIDKFILYMKNYSFEVAV
Sbjct:    1 MEEAKSYEEKFEKIKEIYDQLTGMIQSNGINLVNDQNLNNMIVSLCQRFELKMKSKLTLGVIFDCKYNEPCLIDALLNEKVSPLLDSKYPYVIQGEESVKETRVDHSSKDIKMISVPNEKWKSFNNSVMLLSNNDFKDFLSQISLKSVFDPDVLVLVLKSADELQDPKIQSFISSIKNQNFDPTFLLVLNDAESIDCTVYDYCDVCYPENVRQYLQDAQMNLENRIFKISASKILRSGGDPQAMSAENEHLAKNFTDFKEVFQRDLDIDNVMDRFYRTAQVIGESMDELRKTFDENKLKEVITECETSLVKESSGVIEDIQNQKSNTLKDVNQILDDRNNDENEFLRSILKKVMKQKCGNLRQDLEGKITKIIQKIKDKNYNKEVSTMSRNIFTKEYLNEEKLENNIDDFISNEIDEFKLMDIKKENMDFGKINVEEIDFDKLRNSANQKEKKQAKTVLYKFLYSWKTAIFKIYNVAENAYKTFTAAFKKKVVNVVEDVKKTIDFTVKFSKELHLRHMVKECRKMKQVIETKRKQIRDGIHLHVDLINDKLISIDNEDLKSEKMGNLLGDLMENFEKSCNMAALKHELYTQMQNTGSSELSQKITDHFADQYQKKYLTSAEVDKFDKQIKDQMGKLYKKIDEKKFYVHSKEDFFDIDNENPKTLEELNVMRKEKRSIKTSELMMQLHSTTNDMVTLLNETSNKLNEGIDKFILYMKNYSFEVAV 724
The following BLAST results are available for this feature:
BLAST of SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 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 SMED30000132 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000017239.10.000e+099.03SMESG000017239.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000132 ID=SMED30000132|Name=SMED30000132|organism=Schmidtea mediterranea sexual|type=transcript|length=2726bp
TTATGTTTACATCACCGGTTGATGAAACTGCACAAATTCAAATGAGACTG
CACACGGCAATCTTGGTGGATTTATTTTTAGTATATTCATTATTTGCACT
TATTATTGATTATTTAAGTCCTTTTTACAAGTGCTGAATATTTGAATTCG
GAAATATTATTCTTTGAGCAGAAGATAACATTTCTCATGGAAGAAGCGAA
GAGTTATGAAGAAAAATTTGAAAAAATTAAAGAAATCTATGACCAGTTGA
CTGGCATGATCCAGAGTAACGGAATAAATTTGGTCAACGATCAGAACCTG
AATAACATGATTGTTAGTCTTTGTCAAAGATTCGAATTGAAAATGAAGTC
TAAGTTGACTCTTGGTGTTATATTCGATTGCAAATACAATGAACCGTGCC
TGATCGACGCCCTACTAAACGAAAAGGTCAGTCCGTTGCTCGATTCTAAA
TATCCATATGTAATTCAAGGTGAAGAATCTGTAAAGGAGACGAGAGTTGA
CCACAGTAGCAAAGATATTAAAATGATTTCCGTACCAAATGAGAAATGGA
AATATTTCAATAATTCTGTAATGCTTCTTTCCAATAATGACTTCAAGGAC
TTCCTGTCTCAAATTAGTTTGAAAAGCGTATTTGATCCTGATGTGCTCGT
TCTGGTACTGAAATCAGCAGATGAACTCCAAGACCCTAAAATTCAATCAT
TTATATCATCCATTAAAAATCAGAATTTTGATCCAACCTTCCTATTGGTG
CTTAATGACGCGGAATCAATTGATTGCACCGCTTATGATTATTGCGATGT
CTGCTATCCGGAAAATGTCAGACAATATCTACAAGATGCTCAAATGAATT
TAGAAAACCGAATATTTAAGATATCTGCATCGAAAATTCTCAGATCCGGT
GGAGATCCCCAAGCCATGTCCGCCGAAAACGAACATCTCGCTAAGAATTT
TACTGATTTCAAAGAAGTCTTCCAGCGCGATTTAGACATCGACAACGTGA
TGGACCGGTTTTACAGAACTGCTCAAGTCATTGGCGAGTCCATGGACGAA
CTGCGTAAAACCTTTGACGAGAACAAATTAAAAGAAGTGATAACTGAATG
CGAAACCTCACTCGTCAAGGAATCCAGCGGAGTCATTGAAGACATTCAAA
ATCAAAAGTCAAACACATTGAAAGACGTAAAACAAATTTTTGACGACCGA
AATAATGACGAAAACGAATTTCTGCGAAGTATATTAAAGAAAGTCATGAA
GCAAAAATGTGGGAATCTCCGTCAGGATTTGGAAGGGAAAATCACGAAAA
TCATTCAGAAAATCAAGGATAAAAATTATAATAAGGAAGTGAGCGCCATG
TCAAGGAACATTTTCACCAAAGAATATCTCAATGAAGAAAAACTTGAGAA
CAATATAGATGATTTTATTTCCAATGAAATTGATGAGTTCAAACTCATGG
ATATCAAGAAAGAAAATATGGACTTTGGTAAAATCAATGTCGAAGAGATT
GATTTCGATAAGTTGAGGAATTCCGCGAATCAAAAAGAAAAAAAACAAGC
AAAAACGGTCTTGTACAAATTTTTGTACTCCTGGAAAACTGCCATCTTTA
AGATTTACAATGTTGCGGAAAATGCTTACAAGATCTTCACTGCAGCTTTC
AAGAAAAAAGTTGTAAATGTTGTTGAAGATGTCAAGAAAACCATCGATTT
TACTGTGAAATTTTCAAAAGAACTCCATTTGCGACATATGGTAAAGGAGT
GCCGGAAAATGAAGCAGGTCATTGAGACAAAAAGAAAACAAATCAGAGAC
GGAATCCATTTGCACGTTGACTTGATAAATGACAAATTAATTTCCATTGA
CAATGAGGATCTCAAAAGCGAGAAAATGGGAAATTTACTGGGAGACTTGA
TGGAAAACTTTGAGAAATCCTGTAACATGGCCGCCTTGAAGCATGAATTA
TATACGCAAATGCAGAACACCGGATCAAGTGAGCTGAGTCAGAAAATTAC
GGATCATTTTGCGGATCAGTATCAAAAAAAATATTTGACATCAGCAGAAG
TTGATAAGTTTGATAAACAAATAAAAGACCAAATGGGAAAATTGTACAAG
AAAATTGATGAAAAGAAATTCTATGTGCATTCAAAGGAGGACTTTTTTGA
CATAGATAATGAGAACCCGAAAACACTTGAGGAGTTAAACGTTATGAAGA
AAGAGAAAAGATCCATCAAAACGTCAGAACTGATGATGCAGCTGCATTCT
ACAACAAATGATATGGTGACTTTGCTGAATGAGACCTCAAACAAGCTCAA
TGAAGGCATTGATAAATTCATCCTCTATATGAAAAACTATTCCTTTGAGG
TCGCAGTGTAAATTATCGGGACAATGGAAACGGAGGGGCCTGAATGATTC
ATGAATCCTTAGTGATAACCGCTTATAAATATCCTTTTGTAGTGTACCTC
TATTGGCATTATTAGGACATTGAATGAGCATTTTGTTGATGTATAAATGG
TGGCTGCGCATCTCCGTTGGCCACCCGTTCATTGCCGCCGACACAAAATG
AGAACTCCTACCAAGCCTCGATTCATATGCATATATTACTATATGTATTC
CTCTATATCTCTCTCTTGCGTCTCAATTCAGTTTACGTGGAAATTCAGTT
AGGAAATAAACTAGAAATAATAAATAGAAAACATATAAAAAATAAGTGAA
AAATAACATTTGAAAGGCGGTTCCGA
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protein sequence of SMED30000132-orf-1

>SMED30000132-orf-1 ID=SMED30000132-orf-1|Name=SMED30000132-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=725bp
MEEAKSYEEKFEKIKEIYDQLTGMIQSNGINLVNDQNLNNMIVSLCQRFE
LKMKSKLTLGVIFDCKYNEPCLIDALLNEKVSPLLDSKYPYVIQGEESVK
ETRVDHSSKDIKMISVPNEKWKYFNNSVMLLSNNDFKDFLSQISLKSVFD
PDVLVLVLKSADELQDPKIQSFISSIKNQNFDPTFLLVLNDAESIDCTAY
DYCDVCYPENVRQYLQDAQMNLENRIFKISASKILRSGGDPQAMSAENEH
LAKNFTDFKEVFQRDLDIDNVMDRFYRTAQVIGESMDELRKTFDENKLKE
VITECETSLVKESSGVIEDIQNQKSNTLKDVKQIFDDRNNDENEFLRSIL
KKVMKQKCGNLRQDLEGKITKIIQKIKDKNYNKEVSAMSRNIFTKEYLNE
EKLENNIDDFISNEIDEFKLMDIKKENMDFGKINVEEIDFDKLRNSANQK
EKKQAKTVLYKFLYSWKTAIFKIYNVAENAYKIFTAAFKKKVVNVVEDVK
KTIDFTVKFSKELHLRHMVKECRKMKQVIETKRKQIRDGIHLHVDLINDK
LISIDNEDLKSEKMGNLLGDLMENFEKSCNMAALKHELYTQMQNTGSSEL
SQKITDHFADQYQKKYLTSAEVDKFDKQIKDQMGKLYKKIDEKKFYVHSK
EDFFDIDNENPKTLEELNVMKKEKRSIKTSELMMQLHSTTNDMVTLLNET
SNKLNEGIDKFILYMKNYSFEVAV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell