SMED30002356

Overview
NameSMED30002356
Smed IDSMED30002356
Length (bp)628
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 SMED30002356 (SMED30002356) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002356 (SMED30002356) 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 SMED30002356 (SMED30002356) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002356 (SMED30002356) 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



SMED30002356

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30002356h1SMcG0016180 dd_Smed_v4_4492_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002356h1SMcG0016180 dd_Smed_v4_4492_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30002356h1SMcG0016180 SMED30002356smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30002356h1SMcG0016180 SMED30002356smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Category 3 cellSMED30002356h1SMcG0016180 dd_Smed_v6_4492_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30002356h1SMcG0016180 dd_Smed_v4_4492_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
SMED30002356 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002384:8070..8791 +3013
Homology
[Close]
BLAST of SMED30002356 vs. TrEMBL
Match: I1ZI82 (Uncharacterized protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 80.8777 bits (198), Expect = 5.969e-16
Identity = 34/93 (36.56%), Postives = 58/93 (62.37%), Query Frame = 3 
Query:  219 CAKLMVKLDTECDRKYESFDEDCDGNYSQLFKTCDVNYSKLDAKCQMNLSKSCIRRFGDPNIFCLEAYDQITFSCNKRLAILDAHCDHLYRKL 497
            C+ ++ ++DTECD KY   D +CD +Y  + + CD+ Y+ L  +C++ L++ CI+R+G+ +  CLE+   I   C ++   +D HCD LY  L
Sbjct:   28 CSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 120
[Close]
BLAST of SMED30002356 vs. Planmine SMEST
Match: SMESG000069796.1 (SMESG000069796.1)

HSP 1 Score: 281.182 bits (718), Expect = 4.646e-98
Identity = 136/136 (100.00%), Postives = 136/136 (100.00%), Query Frame = 3 
Query:  105 MKLSVFWVLFLVFHLNSAKTENTAKGISGGLIGISWKECAKLMVKLDTECDRKYESFDEDCDGNYSQLFKTCDVNYSKLDAKCQMNLSKSCIRRFGDPNIFCLEAYDQITFSCNKRLAILDAHCDHLYRKLDNCNL 512
            MKLSVFWVLFLVFHLNSAKTENTAKGISGGLIGISWKECAKLMVKLDTECDRKYESFDEDCDGNYSQLFKTCDVNYSKLDAKCQMNLSKSCIRRFGDPNIFCLEAYDQITFSCNKRLAILDAHCDHLYRKLDNCNL
Sbjct:    1 MKLSVFWVLFLVFHLNSAKTENTAKGISGGLIGISWKECAKLMVKLDTECDRKYESFDEDCDGNYSQLFKTCDVNYSKLDAKCQMNLSKSCIRRFGDPNIFCLEAYDQITFSCNKRLAILDAHCDHLYRKLDNCNL 136
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BLAST of SMED30002356 vs. Planmine SMEST
Match: SMESG000021388.1 (SMESG000021388.1)

HSP 1 Score: 119.013 bits (297), Expect = 3.211e-34
Identity = 58/132 (43.94%), Postives = 82/132 (62.12%), Query Frame = 3 
Query:  111 LSVFWVLFLVFHLNSAKTENTAKGISGGLIGISWKECAKLMVKLDTECDRKYESFDEDCDGNYSQLFKTCDVNYSKLDAKCQMNLSKSCIRRFGDPNIFCLEAYDQITFSCNKRLAILDAHCDHLYRKLDNC 506
            +  F V   V  +N  ++    K          W +C K + K+D ECD+KY+  D DC+G+Y QL+KTCDVNY KL  +CQM LSK+CI+++G  +  C++AY +I  SC+KR A LD +CD LY K +NC
Sbjct:    5 IYAFSVTLAVLRVNCLESPKVFKDEIVNNYEKKWMKCTKFLDKVDAECDKKYDLLDNDCNGSYKQLYKTCDVNYLKLSGRCQMRLSKNCIKKYGKLDRHCIKAYGEIDESCDKRYAKLDPYCDALYTKEENC 136
[Close]
BLAST of SMED30002356 vs. Planmine SMEST
Match: SMESG000072142.1 (SMESG000072142.1)

HSP 1 Score: 95.9005 bits (237), Expect = 2.315e-25
Identity = 50/134 (37.31%), Postives = 75/134 (55.97%), Query Frame = 3 
Query:  105 MKLSVFWVLFLVFHLNSAKTENTAKGISGGLIGISWKECAKLMVKLDTECDRKYESFDEDCDGNYSQLFKTCDVNYSKLDAKCQMNLSKSCIRRFGDPNIFCLEAYDQITFSCNKRLAILDAHCDHLYRKLDNC 506
            MKL +    F+   L + +  + +K  +         +C  ++ K+D ECDRKY   D  CD  Y+ L KTCD+NY KL  +C+ N+S  CI ++G  +  CL AYD++   C+KR  +LD HCD LY+  + C
Sbjct:    1 MKLMIQIGFFMTLALLNVECVSKSKNSA---------DCLTMLDKIDRECDRKYLVLDNHCDSRYAHLHKTCDINYDKLSGRCKNNMSMRCILKYGRLDRKCLGAYDRVDTFCDKRYNVLDTHCDELYKIQEKC 125
[Close]
BLAST of SMED30002356 vs. Planmine SMEST
Match: SMESG000072142.1 (SMESG000072142.1)

HSP 1 Score: 95.5153 bits (236), Expect = 3.456e-25
Identity = 50/134 (37.31%), Postives = 76/134 (56.72%), Query Frame = 3 
Query:  105 MKLSVFWVLFLVFHLNSAKTENTAKGISGGLIGISWKECAKLMVKLDTECDRKYESFDEDCDGNYSQLFKTCDVNYSKLDAKCQMNLSKSCIRRFGDPNIFCLEAYDQITFSCNKRLAILDAHCDHLYRKLDNC 506
            +++  F  L L+     +K++N+A             +C  ++ K+D ECDRKY   D  CD  Y+ L KTCD+NY KL  +C+ N+S  CI ++G  +  CL AYD++   C+KR  +LD HCD LY+  + C
Sbjct:    2 IQIGFFMTLALLNVECVSKSKNSA-------------DCLTMLDKIDRECDRKYLVLDNHCDSRYAHLHKTCDINYDKLSGRCKNNMSMRCILKYGRLDRKCLGAYDRVDTFCDKRYNVLDTHCDELYKIQEKC 122
[Close]
BLAST of SMED30002356 vs. Planmine SMEST
Match: SMESG000024754.1 (SMESG000024754.1)

HSP 1 Score: 87.8113 bits (216), Expect = 3.606e-22
Identity = 47/134 (35.07%), Postives = 73/134 (54.48%), Query Frame = 3 
Query:  105 MKLSVFWVLFLVFHLNSAKTENTAKGISGGLIGISWKECAKLMVKLDTECDRKYESFDEDCDGNYSQLFKTCDVNYSKLDAKCQMNLSKSCIRRFGDPNIFCLEAYDQITFSCNKRLAILDAHCDHLYRKLDNC 506
            MKL +   L +V  L + +  + +K            +C  ++ K+D ECD++Y   D  CD +Y+ L K CD+ Y  L  +C+  LS  CIR++G  +  CL AYD++   C+KR  +LD HCD LY+  + C
Sbjct:    1 MKLMIQIGLLVVLALINVECVSKSK---------KAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLRAYDKVDSYCDKRYNVLDTHCDGLYKLQEKC 125
The following BLAST results are available for this feature:
BLAST of SMED30002356 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 SMED30002356 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 SMED30002356 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 SMED30002356 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 SMED30002356 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 SMED30002356 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 SMED30002356 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 SMED30002356 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZI825.969e-1636.56Uncharacterized protein (Fragment) OS=Schmidtea me... [more]
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BLAST of SMED30002356 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 SMED30002356 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 SMED30002356 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 SMED30002356 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 SMED30002356 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 SMED30002356 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000069796.14.646e-98100.00SMESG000069796.1[more]
SMESG000021388.13.211e-3443.94SMESG000021388.1[more]
SMESG000072142.12.315e-2537.31SMESG000072142.1[more]
SMESG000072142.13.456e-2537.31SMESG000072142.1[more]
SMESG000024754.13.606e-2235.07SMESG000024754.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002356 ID=SMED30002356|Name=SMED30002356|organism=Schmidtea mediterranea sexual|type=transcript|length=628bp
CTTTTGGTTAATAAATTGCGTAGTAACGCAGCTCTATTGACGGAGCCCAC
AGTCAAAACAGTTTAAAACTACAATTTGTGAGTGAAACTGACAAATACGC
AAATATGAAATTGTCAGTTTTTTGGGTCTTGTTTTTAGTTTTTCATCTAA
ATAGCGCGAAAACAGAGAACACGGCAAAAGGAATTTCCGGAGGTCTCATC
GGAATATCTTGGAAGGAATGCGCAAAGCTGATGGTGAAGTTAGACACAGA
GTGCGATAGGAAATACGAAAGTTTCGACGAAGATTGCGATGGAAATTACA
GTCAACTTTTTAAGACCTGTGATGTCAACTATTCAAAGCTTGATGCAAAA
TGTCAAATGAACCTTTCCAAGAGCTGCATTAGAAGATTCGGTGACCCCAA
TATCTTCTGTTTAGAGGCCTATGACCAGATTACGTTTTCGTGCAACAAAC
GACTTGCCATTTTGGATGCTCACTGCGATCATTTGTATAGAAAACTGGAT
AATTGCAATTTATAAGTATTTGAAATGGAACAAAATCACTGGGCAAATAA
ATTTTGCGCGGAATTCAAAACTATATATTGAAAAACATAATTAATTAATA
AATTATCATTCTTTTCTTTCAAAAAAAA
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protein sequence of SMED30002356-orf-1

>SMED30002356-orf-1 ID=SMED30002356-orf-1|Name=SMED30002356-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=137bp
MKLSVFWVLFLVFHLNSAKTENTAKGISGGLIGISWKECAKLMVKLDTEC
DRKYESFDEDCDGNYSQLFKTCDVNYSKLDAKCQMNLSKSCIRRFGDPNI
FCLEAYDQITFSCNKRLAILDAHCDHLYRKLDNCNL*
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Aliases
The feature 'SMED30002356' has the following synonyms
Synonym
prog1-6
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000035Category 3 cell
PLANA:0002032epidermal cell
PLANA:0002142parenchyma
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.842