SMED30010730

Overview
NameSMED30010730
Smed IDSMED30010730
Length (bp)388
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30010730 (SMED30010730) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010730 (SMED30010730) in cells (dots) of each of the 12 neoblast clusters.

 

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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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Anatomical Expression

PAGE et. al., 2020




SMED30010730

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30010730 Contig18286newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010730 Contig18286uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010730 Contig17886uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010730 Contig17886newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010730 Contig18600newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010730 Contig18600uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010730 Contig18071uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010730 Contig18071newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
early male germ cellSMED30010730 Contig5654_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30010730 vs. Planmine SMEST
Match: SMESG000074160.1 (SMESG000074160.1)

HSP 1 Score: 166.392 bits (420), Expect = 1.452e-48
Identity = 94/129 (72.87%), Postives = 116/129 (89.92%), Query Frame = 1
Query:    1 ELMKETIKTKMMREKWENQMEQRIVYPQGKEKPYKEREEELMKEFIQNQTRITNQRKEIQALEQDKQDQQNEIEKLQEIIKDKEAEMQTEGEEMCKILNRTQEELEQIRTKYLVERTKRTSMEQAKEWA 387
            ELM+ET+KTKMM+EKWE Q+EQ+I+YP+GKEK Y+EREEE+MKEF+QNQTRI NQRKEIQ LEQ+KQDQQ+EIEKL+E+IKDKEAE++ EGEE  KI+ + QEE+ QI T+Y +E+TKRT MEQAKEWA
Sbjct: 5004 ELMQETLKTKMMKEKWEKQLEQKIIYPEGKEKTYQEREEEMMKEFMQNQTRIKNQRKEIQTLEQEKQDQQSEIEKLREVIKDKEAEIREEGEETIKIIQQMQEEIGQISTQYRIEKTKRTHMEQAKEWA 5132          
BLAST of SMED30010730 vs. Planmine SMEST
Match: SMESG000053822.1 (SMESG000053822.1)

HSP 1 Score: 160.229 bits (404), Expect = 2.496e-46
Identity = 90/129 (69.77%), Postives = 115/129 (89.15%), Query Frame = 1
Query:    1 ELMKETIKTKMMREKWENQMEQRIVYPQGKEKPYKEREEELMKEFIQNQTRITNQRKEIQALEQDKQDQQNEIEKLQEIIKDKEAEMQTEGEEMCKILNRTQEELEQIRTKYLVERTKRTSMEQAKEWA 387
            EL++ET+KTKMM+EKWE Q+EQ+I YP+GKEK Y+EREEE+MKEF+QNQTRI NQRKEI+ LEQ+KQDQQ+EIE+L+E+IKDKEAE++ EGEE  KI+ + QEE+ QI T+Y +E+TKRT +EQAKEWA
Sbjct: 5024 ELVQETLKTKMMKEKWEKQLEQKITYPEGKEKTYQEREEEMMKEFMQNQTRIINQRKEIRMLEQEKQDQQSEIERLREVIKDKEAEIREEGEETIKIIQQMQEEIGQISTQYRIEKTKRTHLEQAKEWA 5152          
BLAST of SMED30010730 vs. Planmine SMEST
Match: SMESG000066529.1 (SMESG000066529.1)

HSP 1 Score: 158.688 bits (400), Expect = 6.824e-46
Identity = 90/129 (69.77%), Postives = 114/129 (88.37%), Query Frame = 1
Query:    1 ELMKETIKTKMMREKWENQMEQRIVYPQGKEKPYKEREEELMKEFIQNQTRITNQRKEIQALEQDKQDQQNEIEKLQEIIKDKEAEMQTEGEEMCKILNRTQEELEQIRTKYLVERTKRTSMEQAKEWA 387
            EL++ET+KTKMM+EKWE Q+EQ++ YP+GKEK Y+EREEE MKEF+QNQTRI NQRKEIQ LEQ+KQDQQ+EIE+L+E+IKDKEAE++ EGEE  KI+ + QEE+ QI T+Y +E+TKRT +EQAKEWA
Sbjct: 4236 ELVQETLKTKMMKEKWEKQLEQKVTYPEGKEKTYQEREEERMKEFMQNQTRIKNQRKEIQTLEQEKQDQQSEIERLREVIKDKEAEIREEGEETIKIIQQMQEEIGQISTQYRIEKTKRTHLEQAKEWA 4364          
BLAST of SMED30010730 vs. Planmine SMEST
Match: SMESG000066529.1 (SMESG000066529.1)

HSP 1 Score: 158.688 bits (400), Expect = 6.891e-46
Identity = 90/129 (69.77%), Postives = 114/129 (88.37%), Query Frame = 1
Query:    1 ELMKETIKTKMMREKWENQMEQRIVYPQGKEKPYKEREEELMKEFIQNQTRITNQRKEIQALEQDKQDQQNEIEKLQEIIKDKEAEMQTEGEEMCKILNRTQEELEQIRTKYLVERTKRTSMEQAKEWA 387
            EL++ET+KTKMM+EKWE Q+EQ++ YP+GKEK Y+EREEE MKEF+QNQTRI NQRKEIQ LEQ+KQDQQ+EIE+L+E+IKDKEAE++ EGEE  KI+ + QEE+ QI T+Y +E+TKRT +EQAKEWA
Sbjct: 4256 ELVQETLKTKMMKEKWEKQLEQKVTYPEGKEKTYQEREEERMKEFMQNQTRIKNQRKEIQTLEQEKQDQQSEIERLREVIKDKEAEIREEGEETIKIIQQMQEEIGQISTQYRIEKTKRTHLEQAKEWA 4384          
BLAST of SMED30010730 vs. Planmine SMEST
Match: SMESG000066529.1 (SMESG000066529.1)

HSP 1 Score: 158.688 bits (400), Expect = 6.891e-46
Identity = 90/129 (69.77%), Postives = 114/129 (88.37%), Query Frame = 1
Query:    1 ELMKETIKTKMMREKWENQMEQRIVYPQGKEKPYKEREEELMKEFIQNQTRITNQRKEIQALEQDKQDQQNEIEKLQEIIKDKEAEMQTEGEEMCKILNRTQEELEQIRTKYLVERTKRTSMEQAKEWA 387
            EL++ET+KTKMM+EKWE Q+EQ++ YP+GKEK Y+EREEE MKEF+QNQTRI NQRKEIQ LEQ+KQDQQ+EIE+L+E+IKDKEAE++ EGEE  KI+ + QEE+ QI T+Y +E+TKRT +EQAKEWA
Sbjct: 4260 ELVQETLKTKMMKEKWEKQLEQKVTYPEGKEKTYQEREEERMKEFMQNQTRIKNQRKEIQTLEQEKQDQQSEIERLREVIKDKEAEIREEGEETIKIIQQMQEEIGQISTQYRIEKTKRTHLEQAKEWA 4388          
The following BLAST results are available for this feature:
BLAST of SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 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 SMED30010730 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074160.11.452e-4872.87SMESG000074160.1[more]
SMESG000053822.12.496e-4669.77SMESG000053822.1[more]
SMESG000066529.16.824e-4669.77SMESG000066529.1[more]
SMESG000066529.16.891e-4669.77SMESG000066529.1[more]
SMESG000066529.16.891e-4669.77SMESG000066529.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010730 ID=SMED30010730|Name=SMED30010730|organism=Schmidtea mediterranea sexual|type=transcript|length=388bp
GAATTAATGAAAGAAACAATTAAAACAAAAATGATGAGAGAAAAGTGGGA
AAACCAGATGGAACAGCGAATAGTGTACCCACAAGGGAAAGAGAAACCTT
ATAAAGAACGAGAAGAAGAACTGATGAAGGAATTTATTCAGAATCAGACG
AGAATCACAAATCAAAGAAAAGAAATCCAGGCATTAGAACAAGACAAACA
AGATCAACAAAACGAAATAGAGAAACTCCAAGAAATAATAAAAGATAAAG
AAGCAGAAATGCAAACAGAAGGAGAAGAAATGTGTAAAATCTTAAACCGA
ACACAAGAAGAATTGGAACAAATACGAACCAAATATTTGGTGGAAAGAAC
AAAGAGAACGAGCATGGAACAAGCCAAGGAATGGGCAA
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protein sequence of SMED30010730-orf-1

>SMED30010730-orf-1 ID=SMED30010730-orf-1|Name=SMED30010730-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=129bp
ELMKETIKTKMMREKWENQMEQRIVYPQGKEKPYKEREEELMKEFIQNQT
RITNQRKEIQALEQDKQDQQNEIEKLQEIIKDKEAEMQTEGEEMCKILNR
TQEELEQIRTKYLVERTKRTSMEQAKEWA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002030early male germ cell