SMED30029201

Overview
NameSMED30029201
Smed IDSMED30029201
Length (bp)825
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 SMED30029201 (SMED30029201) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029201 (SMED30029201) 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 SMED30029201 (SMED30029201) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029201 (SMED30029201) 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



SMED30029201

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30029201h1SMcG0022571 SmedASXL_018799SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30029201h1SMcG0022571 SmedASXL_018799SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30029201h1SMcG0022571 dd_Smed_v4_1043_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30029201h1SMcG0022571 dd_Smed_v4_1043_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30029201h1SMcG0022570 dd_Smed_v4_3515_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029201h1SMcG0022570 dd_Smed_v4_3515_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30029201h1SMcG0022570 dd_Smed_v4_3515_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30029201 dd_Smed_v4_3946_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30029201 dd_Smed_v4_3946_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30029201h1SMcG0022571 dd_Smed_v6_1043_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30029201h1SMcG0000684 OX_Smed_1.0.21649ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
head regionSMED30029201h1SMcG0022571 OX_Smed_1.0.21649ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30029201 dd_Smed_v4_3946_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
SMED30029201 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000144:32960..33784 +4053
Homology
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BLAST of SMED30029201 vs. Planmine SMEST
Match: SMESG000016306.1 (SMESG000016306.1)

HSP 1 Score: 325.094 bits (832), Expect = 2.090e-113
Identity = 187/202 (92.57%), Postives = 187/202 (92.57%), Query Frame = -2 
Query:   96 KVASPLDGKYSFISLKWTKHELELPCSRTLDIISDLMISRMALKIDYIVIPNVTTGGIQMFSPTLIGLGSIKRSCSIDMKFINETKDMAVKACVSVDEVELNSGVKVDLIVGKFSNIVKLTLDNIVIEITATVPWETGGAXXXXXXXXXXXXXXXIEARGIISGFDSVINVMMKTKMKEAILKLVSKQLPAVINAKLKQYPI 701
            KVASPLD               ELPCSRTLDIISDLMISRMALKIDYIVIPNVTTGGIQMFSPTLIGLGSIKRSCSIDMKFINETKDMAVKACVSVDEVELNSGVKVDLIVGKFSNIVKLTLDNIVIEITATVPWETGGAVVINKVNVVQIKNIKIEARGIISGFDSVINVMMKTKMKEAILKLVSKQLPAVINAKLKQYPI
Sbjct:   16 KVASPLD---------------ELPCSRTLDIISDLMISRMALKIDYIVIPNVTTGGIQMFSPTLIGLGSIKRSCSIDMKFINETKDMAVKACVSVDEVELNSGVKVDLIVGKFSNIVKLTLDNIVIEITATVPWETGGAVVINKVNVVQIKNIKIEARGIISGFDSVINVMMKTKMKEAILKLVSKQLPAVINAKLKQYPI 202
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BLAST of SMED30029201 vs. Planmine SMEST
Match: SMESG000016307.1 (SMESG000016307.1)

HSP 1 Score: 106.301 bits (264), Expect = 4.109e-27
Identity = 53/178 (29.78%), Postives = 104/178 (58.43%), Query Frame = -2 
Query:   96 CSRT-LDIISDLMISRMALKIDYIVIPNVTTGGIQMFSPTLIGLGSIKRSCSIDMKFINETKDMAVKACVSVDEVELNSGVKVDLIVGKFSNIVKLTLDNIVIEITATVPWETGGAXXXXXXXXXXXXXXXIEARGIISGFDSVINVMMKTKMKEAILKLVSKQLPAVINAKLKQYPI 626
            CSR  ++ I D+++ + A +   + +PN T  G+ + SP L    SI RSC+I     + T ++ V+ C ++    + + +KVDL V K   ++K+ L N +I    T+P ++ G +V+    ++ + ++ +E  G I+ FDS +N M+K K++E + +LVS+++P ++N   +++P 
Sbjct:   82 CSRNNMNSIFDVLLRKFATEHKQVALPNATAAGVSILSPILYNTSSIFRSCNITSNLNSTTNNLDVRICFNITNAIILTDLKVDLYVKKMGTLMKVALKNAIINARLTIPLKSKGPMVLKNSTLISLDDVHVENAGFIAKFDSFLNAMLKNKIRETLSRLVSEEIPPIVNEHFRKHPF 259
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BLAST of SMED30029201 vs. Planmine SMEST
Match: SMESG000016301.1 (SMESG000016301.1)

HSP 1 Score: 98.5969 bits (244), Expect = 9.777e-25
Identity = 57/180 (31.67%), Postives = 109/180 (60.56%), Query Frame = -2 
Query:   96 ELPCSRTLDIISDLMISRMALKIDYIVIPNVTTGGIQMFSPTLIGLGSIKRSCSIDMKFINETKDMAVKACVSVDEVELNSGVKVDLIVGKFSNIVKLTLDNIVIEITATVPWETGGAXXXXXXXXXXXXXXXIEARGIISGFDSVINVMMKTKMKEAILKLVSKQLPAVINAKLKQYPI 635
            E  C++  D + D++I R +  ++ + +PN++  GI M S  L GL SIKRSC I  +   +TK++++  C++  E  L + +K++  +  F +  ++ + +I+I + A +P + GG VV+ K+ +V I NI  +  GI+  FD+ +N+M+K+++K+ ++ + + +L   IN  LK Y I
Sbjct:   35 ETTCTKLFDSVVDILIERYSPSMENMKLPNISQSGISMNSTILGGLSSIKRSCQITFEVDPKTKNISIGICLTAKETTLLTFLKIESWIKNFYSFTRVIVTDIIISVKAIIPIKVGGPVVVKKLFIVDIGNIHFDNTGILGSFDTALNLMLKSRLKDMLIDMANNKLTPTINELLKTYEI 214
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BLAST of SMED30029201 vs. Planmine SMEST
Match: SMESG000016305.1 (SMESG000016305.1)

HSP 1 Score: 86.6557 bits (213), Expect = 3.265e-20
Identity = 55/183 (30.05%), Postives = 98/183 (53.55%), Query Frame = -2 
Query:   96 ELELPCS-RTLDIISDLMISRMALKIDYIVIPNVTTGGIQMFSPTLIGLGSIKRSCSIDMKFINETKDMAVKACVSVDEVELNSGVKVDLIVGKFSNIVKLTLDNIVIEITATVPWETGGAXXXXXXXXXXXXXXXIEARGIISGFDSVINVMMKTKMKEAILKLVSKQLPAVINAKLKQYPI 641
            E E  C+ R ++ + D +++R A   D + +PNV    ++M S  L GL S+ RSC   +K   +T +  +  C+ +D+  L++ +   L++  F +  K+ + ++ + I    P  TGG + I  + +  I  IKI   G I   D + N ++ T +K+ I+K+ SK++P  IN  L QYP+
Sbjct:   31 EEEASCTNRLINELVDSILARFAKLFDPLKLPNVIHNRLKMSSTNLTGLESLHRSCDFHIKLNPQTNNFEIAFCIGLDKGVLDTFLDAKLLINSFHSKTKVVIKDLKLNIKLIAPLRTGGPLFIEYIEIANIGAIKINHSGFIGVIDPMANALLNTGIKKMIMKIASKRIPKAINEILIQYPL 213
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BLAST of SMED30029201 vs. Planmine SMEST
Match: SMESG000016304.1 (SMESG000016304.1)

HSP 1 Score: 83.1889 bits (204), Expect = 2.474e-19
Identity = 51/177 (28.81%), Postives = 101/177 (57.06%), Query Frame = -2 
Query:   96 CSRTLDIISDLMISRMALKIDYIVIPNVTTGGIQMFSPTLIGLGSIKRSCSIDMKFINETKDMAVKACVSVDEVELNSGVKVDLIVGKFSNIVKLTLDNIVIEITATVPWETGGAXXXXXXXXXXXXXXXIEARGIISGFDSVINVMMKTKMKEAILKLVSKQLPAVINAKLKQYPI 626
            C+  L+ I D++I +     D + +P++      MF+P + GL S+ RSC+I +     +K++ +  C++V+E                ++ +K+ + ++ + I  T   +TGG +VINK+ +  I  + I+  G +   D ++NVMMKT++K+A++ +++K+LP +IN  L +YP+
Sbjct:   10 CTPNLNSIIDVLIGKYIRMFDPLHLPDINATDTFMFAPNVTGLSSLYRSCNIVVVLDPISKNLTLSFCLAVNE----------------TSYMKIIISDLTVHINVTAQLKTGGPIVINKIGLATIGKVNIDNSGFLGIMDPLVNVMMKTRVKDAVVNIINKKLPNIINETLSKYPL 170
The following BLAST results are available for this feature:
BLAST of SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 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 SMED30029201 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016306.12.090e-11392.57SMESG000016306.1[more]
SMESG000016307.14.109e-2729.78SMESG000016307.1[more]
SMESG000016301.19.777e-2531.67SMESG000016301.1[more]
SMESG000016305.13.265e-2030.05SMESG000016305.1[more]
SMESG000016304.12.474e-1928.81SMESG000016304.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029201 ID=SMED30029201|Name=SMED30029201|organism=Schmidtea mediterranea sexual|type=transcript|length=825bp
CCTCAAAGGATCAGGACGTATCTGATATAAATTTTTATATATTTTATTTA
ATTAATTTTTACAAATTGAACGCACACTAAGTTTAATAAAAATTATATTG
GATATTGCTTCAGTTTGGCGTTGATGACGGCCGGCAACTGCTTACTCACC
AACTTTAAAATCGCCTCTTTCATTTTCGTCTTCATCATCACATTGATGAC
GCTATCAAAACCACTGATGATGCCTCTGGCTTCAATCTTGATGTTCTTGA
TTTGAACAACATTTACTTTATTTATAACAACGGCACCGCCAGTTTCCCAC
GGAACTGTAGCCGTGATTTCAATGACAATATTATCTAATGTCAACTTAAC
AATATTGGAAAATTTTCCAACAATTAAGTCGACTTTTACACCAGAATTTA
GTTCAACTTCGTCTACTGATACGCATGCCTTTACTGCCATGTCTTTTGTT
TCATTAATAAATTTCATATCAATTGAACAGCTTCGCTTGATGGAACCGAG
ACCTATCAAGGTTGGGGAAAACATTTGAATTCCTCCAGTCGTAACATTTG
GAATCACAATATAGTCGATTTTCAATGCCATTCGACTGATCATCAGGTCA
GATATTATGTCTAAAGTCCGGGAACATGGCAGCTCTAATTCATGTTTAGT
CCATTTCAAACTAATAAAACTGTACTTACCGTCCAAGGGTGAAGCGACCT
TTATTAATGGAAACAATAATAATATGAAGAGGCAAATCAGATTCATTTAA
TAAAGATTTCATGGTCAGAATGTGTATTAATGGTAAATAAGGGCATCCGG
TAATTTTCCCCTTACGATTACAACT
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protein sequence of SMED30029201-orf-1

>SMED30029201-orf-1 ID=SMED30029201-orf-1|Name=SMED30029201-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=218bp
MNLICLFILLLFPLIKVASPLDGKYSFISLKWTKHELELPCSRTLDIISD
LMISRMALKIDYIVIPNVTTGGIQMFSPTLIGLGSIKRSCSIDMKFINET
KDMAVKACVSVDEVELNSGVKVDLIVGKFSNIVKLTLDNIVIEITATVPW
ETGGAVVINKVNVVQIKNIKIEARGIISGFDSVINVMMKTKMKEAILKLV
SKQLPAVINAKLKQYPI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR038602Mite_allergen_7_sf
IPR020234Mite_allergen_group-7
IPR019774Aromatic-AA_hydroxylase_C
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
Vocabulary: biological process
TermDefinition
GO:0055114oxidation-reduction process
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR038602Mite allergen, group-7 superfamilyGENE3DG3DSA:3.15.10.50coord: 45..215
e-value: 1.3E-7
score: 33.1
IPR020234Mite allergen, group-7PFAMPF16984Grp7_allergencoord: 69..212
e-value: 6.6E-5
score: 23.0
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.823