SMED30030887

Overview
NameSMED30030887
Smed IDSMED30030887
Length (bp)1314
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 SMED30030887 (SMED30030887) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030887 (SMED30030887) 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 SMED30030887 (SMED30030887) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030887 (SMED30030887) 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



SMED30030887

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30030887 dd_Smed_v4_339_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30030887 dd_Smed_v4_339_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30030887 dd_Smed_v4_339_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30030887 dd_Smed_v4_339_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30030887 dd_Smed_v4_339_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30030887 dd_Smed_v4_339_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30030887 dd_Smed_v6_339_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
musculature systemSMED30030887 dd_Smed_v6_339_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
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BLAST of SMED30030887 vs. Planmine SMEST
Match: SMESG000001257.1 (SMESG000001257.1)

HSP 1 Score: 184.111 bits (466), Expect = 9.965e-51
Identity = 102/173 (58.96%), Postives = 131/173 (75.72%), Query Frame = 3 
Query:  732 YVESNRRLVEKFRKDVAQYXHXXMIQNQRAEDIVRKCRHLEQTWLRPE*VSKLKAEIEVVKNKLAKNDEALRQAEQKTQXXXXXXXXXXXXXXIRTGLIQCGAMLSAEQEAIVIRNVTGKDIGGKILTPGPSHLSEEVPKRN*KRNWPGEMERERLSKLNKARMVGHILNADG 1250
            ++E N +++E+FRKDVA+Y    M+QNQRA  +VR+CR +EQTWL PE V KL+AEIE +  KLA+ +EAL QAEQK +  + E+ +LKL+DEIR GLI C + L AEQEAIVIRNV GKDIG KI+TPG S   EE PKRN +RN  G+ ER+R +K+  ARMVGHIL ++G
Sbjct:  664 FMEQNNKIIERFRKDVAKYHQEAMVQNQRAVALVRRCRRIEQTWLGPEEVIKLRAEIETLNLKLAQKEEALMQAEQKIRTQDSEIVDLKLKDEIRAGLILCESQLPAEQEAIVIRNVVGKDIGVKIITPGTSRPPEEKPKRNRQRNRSGKKERDRQNKVKTARMVGHILKSNG 836
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BLAST of SMED30030887 vs. Planmine SMEST
Match: SMESG000001257.1 (SMESG000001257.1)

HSP 1 Score: 183.726 bits (465), Expect = 1.226e-50
Identity = 102/173 (58.96%), Postives = 131/173 (75.72%), Query Frame = 3 
Query:  732 YVESNRRLVEKFRKDVAQYXHXXMIQNQRAEDIVRKCRHLEQTWLRPE*VSKLKAEIEVVKNKLAKNDEALRQAEQKTQXXXXXXXXXXXXXXIRTGLIQCGAMLSAEQEAIVIRNVTGKDIGGKILTPGPSHLSEEVPKRN*KRNWPGEMERERLSKLNKARMVGHILNADG 1250
            ++E N +++E+FRKDVA+Y    M+QNQRA  +VR+CR +EQTWL PE V KL+AEIE +  KLA+ +EAL QAEQK +  + E+ +LKL+DEIR GLI C + L AEQEAIVIRNV GKDIG KI+TPG S   EE PKRN +RN  G+ ER+R +K+  ARMVGHIL ++G
Sbjct:  680 FMEQNNKIIERFRKDVAKYHQEAMVQNQRAVALVRRCRRIEQTWLGPEEVIKLRAEIETLNLKLAQKEEALMQAEQKIRTQDSEIVDLKLKDEIRAGLILCESQLPAEQEAIVIRNVVGKDIGVKIITPGTSRPPEEKPKRNRQRNRSGKKERDRQNKVKTARMVGHILKSNG 852
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BLAST of SMED30030887 vs. Planmine SMEST
Match: SMESG000063949.1 (SMESG000063949.1)

HSP 1 Score: 178.718 bits (452), Expect = 2.180e-49
Identity = 108/182 (59.34%), Postives = 137/182 (75.27%), Query Frame = 3 
Query:  708 LQCIANT*YVESNRRLVEKFRKDVAQYXHXXMIQNQRAEDIVRKCRHLEQTWLRPE*VSKLKAEIEVVKNKLAKNDEALRQAEQKTQXXXXXXXXXXXXXXIRTGLIQCGAMLSAEQEAIVIRNVTGKDIGGKILTPGPSHLSEEVPKRN*KRNWPGEMERERLSKLNKARMVGHILNADGF 1253
            +QC + T   ES  +++  ++    +Y    + ++QRAE +VRKCRH+EQTWLRPE   K K E++ +K KLA+ DEALRQAE+K Q LEKE+KELKL+DEI T L+Q G  L AEQEAI+IRNVTGKDIG KI+TPG SH   EVPKRN KRN P + ERERL KL+KAR++GHIL+A+GF
Sbjct:  492 VQCGSGTNGTES--QIINNYQS--TEYHREALNESQRAEAMVRKCRHMEQTWLRPETAVKFKNELDGLKAKLAQKDEALRQAEEKAQALEKEVKELKLKDEILTCLVQSGTTLWAEQEAIMIRNVTGKDIGVKIMTPGASHSLVEVPKRNRKRNRPSKKERERLFKLHKARLIGHILDANGF 669
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BLAST of SMED30030887 vs. Planmine SMEST
Match: SMESG000007350.1 (SMESG000007350.1)

HSP 1 Score: 165.236 bits (417), Expect = 3.085e-49
Identity = 90/125 (72.00%), Postives = 107/125 (85.60%), Query Frame = 3 
Query:  735 VESNRRLVEKFRKDVAQYXHXXMIQNQRAEDIVRKCRHLEQTWLRPE*VSKLKAEIEVVKNKLAKNDEALRQAEQKTQXXXXXXXXXXXXXXIRTGLIQCGAMLSAEQEAIVIRNVTGKDIGGKI 1109
            VESNR+++EKFRKD AQY H  M+QNQR E +VRKCRHLEQTWLRPE ++KL+AE+E +K KL + DEALRQAEQK QE EKE+++LKL+ EIRTGL+Q   +LSAEQEAIVIRNVTGKDIG KI
Sbjct:   33 VESNRQMIEKFRKDHAQYHHEAMVQNQRPEALVRKCRHLEQTWLRPEGIAKLRAEVEALKIKLTQKDEALRQAEQKVQEKEKEIRDLKLKYEIRTGLVQSSTILSAEQEAIVIRNVTGKDIGVKI 157
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BLAST of SMED30030887 vs. Planmine SMEST
Match: SMESG000028986.1 (SMESG000028986.1)

HSP 1 Score: 157.918 bits (398), Expect = 1.846e-44
Identity = 88/157 (56.05%), Postives = 120/157 (76.43%), Query Frame = 3 
Query:  738 ESNRRLVEKFRKDVAQYXHXXMIQNQRAEDIVRKCRHLEQTWLRPE*VSKLKAEIEVVKNKLAKNDEALRQAEQKTQXXXXXXXXXXXXXXIRTGLIQCGAMLSAEQEAIVIRNVTGKDIG-GKILTPGPSHLSEEVPKRN*KRNWPGEMERERLSK 1205
            +S+++ +E+FR+D+A Y    + Q QRAE +VRKCR++EQTWLRPE   KLK E++ +KN+LA+ DEALR AEQK Q+LEK++ E KL D IRTGL+Q G  LS EQ+AIV+RN TGKD G G+++T GPSH  E +PKRN ++N P + ERER ++
Sbjct:  124 DSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKEEVDTLKNQLAQKDEALRSAEQKAQDLEKQVAEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIGQMIT-GPSHTPEGLPKRNRRKNRPNKRERERQAR 279
The following BLAST results are available for this feature:
BLAST of SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 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 SMED30030887 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000001257.19.965e-5158.96SMESG000001257.1[more]
SMESG000001257.11.226e-5058.96SMESG000001257.1[more]
SMESG000063949.12.180e-4959.34SMESG000063949.1[more]
SMESG000007350.13.085e-4972.00SMESG000007350.1[more]
SMESG000028986.11.846e-4456.05SMESG000028986.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030887 ID=SMED30030887|Name=SMED30030887|organism=Schmidtea mediterranea sexual|type=transcript|length=1314bp
TTTTTTTTTAACACTTGAATTTTATTCCATTCAATCGATAATTATCACAC
AATAATTGTGGTTTTTCTTGTTAGTTTTGGCAGATCTCCCTCGATGGAGT
AGTAACAATTTATAATTACATTTGTTCCATCGTTTGGGTAACAATATAGA
ACTTGGGCTAGTGAAATATCATGATTATAATTGCTAAGCTCACCATTTCT
TAATTTTTCCTTGTCTTCCATGCTGATTTCGTCCGTCTGGTTTCCATGTG
GAGTGTTGTTCGGATTTCTAGACATTTCAATAGTACCAAAAAAAATATGA
GATTCTCTCCGTGGANNCNCTNTTNNNANCTNTGCNGGTGTGTAAGTTCT
CGTCAGGCAGTGGTGTGCCAGACGTGGTTGCATACAGTTGCTAGGTTGGA
GATATGCCGTTACGTCTCTATTACCGAATNNATNGNCGANNTGTCAGGTC
GATTTTCCATCGGCCGGGTTATATGTGTCGGAATTTATCTTAACATTTTT
CAATTAATTCAGTACNGGNNNNNNNNNNNANNNATNNNNTTTCTGGGACA
ACATTGTTCATGATGTAAGATCCTACATGAGAAATAGCGGTGGGATCCGA
CACCAGTTATTTCGTGGACTACTCGTTCCACGTTGGGCATATTTCTCCTT
CGGTTCCAATCTGAATGGATCGCCGCATCTATCCCTGATGAATCTCCTCT
GTGGTAACTTCAATGTATCGCCAATACCTAATATGTGGAATCAAACCGAC
GCTTAGTAGAGAAATTCAGAAAGGACGTCGCTCAATACCNNCATGANGNG
ATGATCCAGAACCAAAGGGCGGAAGATATTGTGCGCAAGTGCCGGCACCT
AGAGCAAACATGGCTCCGTCCAGAATGAGTGTCCAAGTTGAAGGCAGAAA
TAGAAGTGGTGAAAAATAAACTAGCAAAAAATGATGAGGCCCTGAGGCAA
GCCGAACAGAAAACCCAGGAGCTAGAGAAGGAAATGAAAGAGCTGAAATT
AGAAGATGAGATCCGCACCGGACTCATCCAATGTGGGGCAATGCTATCGG
CCGAGCAAGAGGCGATTGTAATTCGCAATGTAACCGGGAAGGACATCGGG
GGGAAAATTCTCACTCCAGGACCCTCACATCTGTCGGAGGAAGTGCCGAA
ACGAAATTGAAAAAGAAATTGGCCTGGCGAAATGGAACGCGAGCGGTTAT
CTAAGCTTAACAAAGCTCGGATGGTAGGGCACATTTTAAACGCGGACGGT
TTTTGAACGGCGTGCGACTGACACTGTGATAGTCATATAATTGTTGTATT
TTATTGGATTTATC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000428musculature system
PLANA:0000478pharynx musculature
PLANA:0003116parenchymal cell