SMED30002839

Overview
NameSMED30002839
Smed IDSMED30002839
Length (bp)697
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 SMED30002839 (SMED30002839) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002839 (SMED30002839) 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 SMED30002839 (SMED30002839) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002839 (SMED30002839) 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



SMED30002839

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
Smed sexual biotypeSMED30002839h1SMcG0009360 Contig54932uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002839h1SMcG0009360 Contig54932newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002839h1SMcG0009360 Contig25004newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002839h1SMcG0009360 Contig25004uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30002839h1SMcG0009360 dd_Smed_v4_1388_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002839h1SMcG0009360 dd_Smed_v4_1388_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30002839h1SMcG0009360 dd_Smed_v4_1388_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002839h1SMcG0009360 Contig30742newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002839h1SMcG0009360 Contig30742uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002839h1SMcG0009361 Contig30742newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002839h1SMcG0009361 Contig30742uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
body wall musculatureSMED30002839h1SMcG0009360 dd_Smed_v4_1388_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002839 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000621:30266..33278 +3421
Homology
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BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000079498.1 (SMESG000079498.1)

HSP 1 Score: 360.533 bits (924), Expect = 1.646e-128
Identity = 174/174 (100.00%), Postives = 174/174 (100.00%), Query Frame = 3 
Query:   93 MDVNTVYYTGDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSDFTNKG 614
            MDVNTVYYTGDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSDFTNKG
Sbjct:    1 MDVNTVYYTGDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSDFTNKG 174
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BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000079496.1 (SMESG000079496.1)

HSP 1 Score: 166.007 bits (419), Expect = 1.061e-51
Identity = 83/157 (52.87%), Postives = 106/157 (67.52%), Query Frame = 3 
Query:  120 GDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSED-GIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIR 587
             D T   Y C ND+Y +L A+ +GSDL+L     ++      + F+E HY   D  +P+SVIQH+VS KA+FYD   + F LKS  +N++ ITDPNSNFLL+VGGGSTV CFSN++TT TLA VG NL TY NTT PPW  S   L++S  DF+WIR
Sbjct:   14 SDSTNWVYSCKNDEYKYLKADANGSDLKLWTMVEDSCENYTNYEFREYHYRCNDCNVPVSVIQHKVSKKAIFYDGTTERFVLKSVPENIEKITDPNSNFLLFVGGGSTVACFSNRRTTRTLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIR 170
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BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000079496.1 (SMESG000079496.1)

HSP 1 Score: 166.007 bits (419), Expect = 1.185e-51
Identity = 83/157 (52.87%), Postives = 106/157 (67.52%), Query Frame = 3 
Query:  120 GDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSED-GIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIR 587
             D T   Y C ND+Y +L A+ +GSDL+L     ++      + F+E HY   D  +P+SVIQH+VS KA+FYD   + F LKS  +N++ ITDPNSNFLL+VGGGSTV CFSN++TT TLA VG NL TY NTT PPW  S   L++S  DF+WIR
Sbjct:   13 SDSTNWVYSCKNDEYKYLKADANGSDLKLWTMVEDSCENYTNYEFREYHYRCNDCNVPVSVIQHKVSKKAIFYDGTTERFVLKSVPENIEKITDPNSNFLLFVGGGSTVACFSNRRTTRTLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIR 169
[Close]
BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000025939.1 (SMESG000025939.1)

HSP 1 Score: 75.8702 bits (185), Expect = 5.943e-17
Identity = 50/158 (31.65%), Postives = 87/158 (55.06%), Query Frame = 3 
Query:  132 ECTYCCYNDKYYWLTANTDGSDLRLLN-TKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSS-EDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSD 599
            E  +CCY ++  +L A++D   L+L N +  ++ H +   +F++ +Y   D + +SVI+H+ SGK ++YD+++K F LK + E + D     +SNF+L  GG S + C SN +T  TLAY      T      P    S+D ++D     +W + + +
Sbjct:   20 EYVFCCYLNENAYLVADSDMVHLQLTNFSMLQSTHNV---IFQQ-YYLDSDNVHLSVIKHKRSGKFIYYDEDSKDFILKENPEVHFDKF---DSNFILARGGNSNIFCLSNLETNATLAYNNGQFQTLHIPEKPWLYSSEDLIDDKMKHIAWKKKSEN 170
[Close]
BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000025939.1 (SMESG000025939.1)

HSP 1 Score: 76.2554 bits (186), Expect = 6.260e-17
Identity = 50/158 (31.65%), Postives = 87/158 (55.06%), Query Frame = 3 
Query:  132 ECTYCCYNDKYYWLTANTDGSDLRLLN-TKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSS-EDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSD 599
            E  +CCY ++  +L A++D   L+L N +  ++ H +   +F++ +Y   D + +SVI+H+ SGK ++YD+++K F LK + E + D     +SNF+L  GG S + C SN +T  TLAY      T      P    S+D ++D     +W + + +
Sbjct:   40 EYVFCCYLNENAYLVADSDMVHLQLTNFSMLQSTHNV---IFQQ-YYLDSDNVHLSVIKHKRSGKFIYYDEDSKDFILKENPEVHFDKF---DSNFILARGGNSNIFCLSNLETNATLAYNNGQFQTLHIPEKPWLYSSEDLIDDKMKHIAWKKKSEN 190
The following BLAST results are available for this feature:
BLAST of SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 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 SMED30002839 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000079498.11.646e-128100.00SMESG000079498.1[more]
SMESG000079496.11.061e-5152.87SMESG000079496.1[more]
SMESG000079496.11.185e-5152.87SMESG000079496.1[more]
SMESG000025939.15.943e-1731.65SMESG000025939.1[more]
SMESG000025939.16.260e-1731.65SMESG000025939.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002839 ID=SMED30002839|Name=SMED30002839|organism=Schmidtea mediterranea sexual|type=transcript|length=697bp
TTTTAAAATAAAATAAAATCAAATAAATAATAGTTTTAAGATCATTTTTA
GTTATATTTAATTTTATAATAGACAGAAAAAGGACAGCCAAGATGGATGT
AAATACTGTATATTACACCGGTGACTTTACAGAATGCACATATTGCTGTT
ATAATGACAAATACTACTGGCTGACGGCGAATACGGACGGGAGTGATTTA
AGACTGTTGAATACCAAAACCGAAGCTGGTCATGTAATAGAACCTTTCAT
GTTCAAAGAACTTCATTACCATTCTGAAGACGGAATACCAATATCAGTCA
TCCAGCATGAGGTCAGTGGCAAGGCTCTGTTTTATGATGATGAAAACAAA
ACTTTCGAGTTAAAAAGTAGTGAAGACAATTTGGATAATATCACAGATCC
AAATTCAAACTTCTTATTGTATGTTGGAGGAGGATCAACAGTTACATGCT
TCTCAAATAAAAAAACTACGGGAACACTCGCTTATGTTGGCCTAAATCTC
ATAACTTATGAAAATACTACTTCTCCACCTTGGACATTGTCTCAAGATAC
ATTAGAAGATTCAAGAAACGATTTTTCGTGGATAAGAAATACATCCGATT
TCACAAATAAAGGATAACAACTTGATTTTTAAAAACTAATTTGCGCAATG
AATCAAATAGATAAAATAAAAAAATTTCGTTTTTTAACATTTAAAAA
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protein sequence of SMED30002839-orf-1

>SMED30002839-orf-1 ID=SMED30002839-orf-1|Name=SMED30002839-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=175bp
MDVNTVYYTGDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIE
PFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNI
TDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLS
QDTLEDSRNDFSWIRNTSDFTNKG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000240body wall musculature
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR019774Aromatic-AA_hydroxylase_C
Vocabulary: biological process
TermDefinition
GO:0055114oxidation-reduction process
Vocabulary: molecular function
TermDefinition
GO:0016714oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen