SMED30033178

Overview
NameSMED30033178
Smed IDSMED30033178
Length (bp)3520
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 SMED30033178 (SMED30033178) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033178 (SMED30033178) 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 SMED30033178 (SMED30033178) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033178 (SMED30033178) 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



SMED30033178

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30033178 dd_Smed_v4_25118_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30033178 dd_Smed_v4_25118_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30033178 dd_Smed_v4_25118_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30033178 vs. Planmine SMEST
Match: SMESG000057359.1 (SMESG000057359.1)

HSP 1 Score: 117.087 bits (292), Expect = 4.731e-30
Identity = 67/145 (46.21%), Postives = 86/145 (59.31%), Query Frame = 3 
Query:  246 IINSNYDLAMDAIKDISNELRKLRKENTSLHQQCIQLSRELQRTRATWVEPSRAKKLYQRLTAAQKGWQEEKTLNQTQSTNL-WIGSCRRSQPRGECGHLPIGVCTRASSLPGTRPD*KTTGKPKIHTRPGKAERERRKRQHQAN 677
            +INS    AM+ IK+I  EL+KLR EN +LHQQC+QLS E QR   TW+EPSR K+LYQ+++AAQKG QEEK LNQ Q   +  +     +   G     P+       +           GKPK HTRPG+A+RER K Q Q +
Sbjct:    8 LINS----AMNTIKNIGRELKKLRTENANLHQQCVQLSCEQQRINDTWIEPSRVKRLYQKISAAQKGLQEEKALNQAQKIQIRGLEIAVAASQEGSAVTYPLVFAPTQVTYKEQHGPKNPKGKPKTHTRPGRAKRERTKVQQQKD 148
[Close]
BLAST of SMED30033178 vs. Planmine SMEST
Match: SMESG000021767.1 (SMESG000021767.1)

HSP 1 Score: 118.242 bits (295), Expect = 5.854e-30
Identity = 65/139 (46.76%), Postives = 89/139 (64.03%), Query Frame = 3 
Query:  267 LAMDAIKDISNELRKLRKENTSLHQQCIQLSRELQRTRATWVEPSRAKKLYQRLTAAQKGWQEEKTLNQTQSTNL-----WIGSCRRSQPRG-ECGHLPIGVCTRASSLPGTRPD*KTTGKPKIHTRPGKAERERRKRQ 665
            L MDA++ ISN+L+ LRKE T+LHQQC+QLSRELQR RATW EP+R K+LYQ++ A QKGWQEE+ LNQ Q   +      + + +  Q        +P  V  + ++ P  +P      KPK   RP KAE++R+K+Q
Sbjct:   61 LMMDAMQKISNKLKNLRKEITNLHQQCLQLSRELQRIRATWSEPARVKRLYQKIDAVQKGWQEERFLNQAQKVQIRGLEVAVAASQEGQAVTYPMVFVPAQVAYKNATSPLDQP-----FKPKSRARPEKAEKKRQKQQ 194
[Close]
BLAST of SMED30033178 vs. Planmine SMEST
Match: SMESG000053804.1 (SMESG000053804.1)

HSP 1 Score: 113.62 bits (283), Expect = 4.613e-29
Identity = 66/135 (48.89%), Postives = 83/135 (61.48%), Query Frame = 3 
Query:  273 MDAIKDISNELRKLRKENTSLHQQCIQLSRELQRTRATWVEPSRAKKLYQRLTAAQKGWQEEKTLNQTQST---NLWIGSCRRSQPRGECGHL---PIGVCTRASSLPGTRPD*KTTGKPKIHTRPGKAERERRK 659
            MDAI+ I  EL+KLR+EN  LHQQC+QLSRELQ  +ATW EPSR K LY++  AAQKGWQ+E+TLNQTQ      L +      + R    HL   P  V  +  + P  RP      + K  TRPG+A+R R+K
Sbjct:    1 MDAIQGIGVELKKLRRENDCLHQQCLQLSRELQWIKATWSEPSRVKLLYEKNDAAQKGWQDERTLNQTQRIQIRGLKVAVAADQEGRAVMYHLVFAPAQVAYQNQTSPAERP-----SQQKFRTRPGRAKRARQK 130
[Close]
BLAST of SMED30033178 vs. Planmine SMEST
Match: SMESG000077887.1 (SMESG000077887.1)

HSP 1 Score: 93.5893 bits (231), Expect = 5.174e-29
Identity = 42/73 (57.53%), Postives = 57/73 (78.08%), Query Frame = 3 
Query:  273 MDAIKDISNELRKLRKENTSLHQQCIQLSRELQRTRATWVEPSRAKKLYQRLTAAQKGWQEEKTLNQTQSTNL 491
            MDA++ I  EL+ LRKEN +LHQQC+QLSRELQR +ATW +P+R K+LYQ++  AQKG +EE+  NQ Q+  +
Sbjct:    1 MDAMQKIGKELKDLRKENANLHQQCLQLSRELQRIKATWSDPTRVKRLYQKIDTAQKGCREERVQNQAQNVQI 73

HSP 2 Score: 55.4546 bits (132), Expect = 5.174e-29
Identity = 27/33 (81.82%), Postives = 29/33 (87.88%), Query Frame = 1 
Query:  481 VQICGLEVAVAANQEGSAVTYPLVFAPAQVAYQ 579
            VQI GLE+AVAA QE  AVTYPLVFAPAQVAY+
Sbjct:   71 VQIRGLEIAVAAGQEEQAVTYPLVFAPAQVAYK 103
[Close]
BLAST of SMED30033178 vs. Planmine SMEST
Match: SMESG000022029.1 (SMESG000022029.1)

HSP 1 Score: 112.079 bits (279), Expect = 2.437e-28
Identity = 65/136 (47.79%), Postives = 86/136 (63.24%), Query Frame = 3 
Query:  273 MDAIKDISNELRKLRKENTSLHQQCIQLSRELQRTRATWVEPSRAKKLYQRLTAAQKGWQEEKTLNQTQSTNLWIG---SCRRSQPRGECGHL----PIGVCTRASSLPGTRPD*KTTGKPKIHTRPGKAERERRK 659
            MD+IK+I  E +KLR++N  LHQQC+QLS ELQRT+ATW+E S  K++YQRLTAAQ+GW+EEK LNQ Q   + IG   +   SQ R    +L    P  V  +  + P      +   K K HT+P +AE ERR+
Sbjct:    1 MDSIKEIGLERKKLRRKNIDLHQQCVQLSHELQRTKATWIETSGVKRIYQRLTAAQRGWKEEKALNQAQKVQI-IGIEVAVAASQDRRAVTYLLVFGPAHVAYQDRAFPN-----EPQRKSKTHTKPERAEWERRR 130
The following BLAST results are available for this feature:
BLAST of SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 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 SMED30033178 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057359.14.731e-3046.21SMESG000057359.1[more]
SMESG000021767.15.854e-3046.76SMESG000021767.1[more]
SMESG000053804.14.613e-2948.89SMESG000053804.1[more]
SMESG000077887.15.174e-2957.53SMESG000077887.1[more]
SMESG000022029.12.437e-2847.79SMESG000022029.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033178 ID=SMED30033178|Name=SMED30033178|organism=Schmidtea mediterranea sexual|type=transcript|length=3520bp
TTAGAATTACCGTAACCAAGTTACAACATAGTCAGTAATTTAAAAAAAAG
CAAAATTAACAAGGAATTTAATCGTCAGTATATCTGTTATTGAAGGTGAT
AATAATTGTGATCAAGGGGATTTACAAAGTTAATGTGTAGAATAAAGTTG
TTGGTTATTTTTGATTCCTATAATATTTAATGTAAATTGTTTATCTGATT
ATTGAGGTTGATGGTTGATGATCAAGAAATTAGTATCGAGAATAAATTAT
TAACTCTAATTATGATTTAGCCATGGACGCGATAAAAGACATTAGCAACG
AACTGAGAAAGTTGAGGAAGGAGAACACTAGCCTACATCAGCAGTGCATT
CAACTCAGCCGAGAGCTCCAACGGACGAGAGCGACCTGGGTAGAGCCTTC
ACGGGCAAAGAAACTTTACCAAAGATTAACGGCGGCTCAGAAGGGCTGGC
AAGAAGAGAAGACCTTGAACCAGACCCAAAGTACAAATTTGTGGATTGGA
AGTTGCCGTCGCAGCCAACCAAGAGGGGAGTGCGGTCACTTACCCATTGG
TGTTTGCACCCGCGCAAGTAGCTTACCAGGGACAAGACCAGACTAGAAGA
CCACTGGCAAACCGAAAATCCACACAAGGCCGGGAAAAGCCGAACGAGAG
CGCAGAAAACGCCAACACCAAGCGAACTGAGCATGAATGGATTTCTGATC
TTTGTTGAATGTCCGGGTGTGGATAGGAAGTTGTATTTTTATTTGATATT
GTAATAAATGTTTGAGTCTTAATTTGGTTATTATATGATTCGAACACCGT
ACTAAAGATAATGAATTGTATGAAAGTGAGTCATGAGTCGAATGAGTAAA
AATGTGGAAGTAAGGGACTTAAAAAGCAAGACGAGCATATACCAGATCTC
AATCAAATCAGTTTGCTGACTTATATATTGTTAATGTTTCTTACCAGTTG
TTAATTTCTTTTAACTTAATTAAATTCTTTAAATAACATAAATAGACAAA
AACGCGATTGTCATAATTGTTACATAGAATTTTCTTAGAATAATTATTAC
TGAAATATAAAAGTGAAATTCTTTTTCATTTTAAACAATTTACACAAAAG
TTTATTTGAGGAAAACAATTGATTAAAATTGTTGCAGAATTCTTCCACTT
TTCGTTATCGTGAAGTAGTTGCCTGTTTGATCTCCTTTATTTCATCACAC
TCAAGAGAATGAATCATTATATTAAATAAAAATAAAATAAAATAGCATAA
TTTCTTTTACTCTCTTTCCTCGTAAACCTGAAAATCACCTATGATAGAAG
AGCATATTATCTAATGACCGTATTTTTAAGATGTTATTTTGATTCAATTT
TAAATGAATTTATGAACTTTTTATGCCATGCGTATGCAAACTTGTAATAG
TCGAATGTTTTTTTATATATAAACTTAAATTCAAAATATTCCTTCGTTTC
CGTGGTACTTGACTAATACGTGATGCCTCATGATTAAATTTTCATTATCA
CATAATAATCATTAATCTTATAATTGTTCAGAAAAAGAACCGAATTTATT
TGATTATTTATTTATTATATTATTGATATTAATACTATTAATTGTTATCC
ATAATGCTCATTTATGATGTAAAAGTGACTATGACATGCAGGCAAGAAAG
CAAAATTAATGTTTCATCAACTAGCCTAAAACTAGTACTTCGGGTGGGAG
GTACCCGTAGCGAATGGTAGTTCGCCGATTCAGATCTCTTCTTCAAGAAC
CTCAATATCAAACCCTCAGTAGAGAGTGAATGACCATGAGGAAGGAGCAA
ATATTATATATGTAAAGAAAGAAGAATAAATGAATGAGGAAAGAAAGAAG
AATATCACGAGAGTGTGAGTAATCTTCACGAGTACACCTGAAAAATGAAT
AAATTAATAAAAGAAAAATGTGGGCGTCAGTAATTTTCATAGAACGTAAA
GAACAAAAGAAAGAAGAACCTAGACAACAGAAGGTACTATTTCAGGTATA
AATGCCAAATTACTATCATTAGTGACAAAACTAGGAGTCAAAGAAACTAT
CAAATTACCACTTCATTGTCACTCATATTCCAATAATACATAGATTAACC
CAGGTAATTAATTTTATAAAATAAATTCATAGATAAACAAATCTTAATAA
TGATTCCTTGAATTTATTTATTTAAAAAACTAAATAAAAATATTTTTTTA
TATAAAATTTTATTTTCGTCAGCATCAACAGCAACTGTATTGGTATCTGT
GAAAACTACTAAGAACTAGATCGGATTATTTTTTGCGGTAATTTTTTAAC
ACCCCATTAGTACGTGTGTCTGCGCCACATATATTAGAGTGCCAGGCACG
TGCCACGTTATTGCTTTCATTTTAAAATCATAAAACCTCAACTAATTTTA
TTTTTGAATTATTTAATAAATCCAAACGTACTTACCCGAATTTTATATAC
AAACATATCAAACATATTGATATTGGTCCGAATAACAAAGAATTATATAC
GAAAATAGCTGCAAATCATCATCCCTTATTAATCGATACACAATCTAATC
AACTCTCGTTGGTTATTGAACAATTTCGTGGTAATTAGATTATTTTCGCA
ATTATATTATTCCGGATATTTCATTTGCTATTGATTAAGGTGACTTGTGG
AAAATGGTAAAAATAACAAAAACAGTAATGATGGAAACTGACTACAACTC
CGATGATGACCGAATTGTTAGAAGTAGATGAATCTGTTAGATCGAATGGT
CGATCAAAGTCGTCAAAGCATTGCCTGAAACATCTATGCAAAATTTGCGA
AATGATACATTTTCTGATAGATTATTGCCGGTTTTTTTAAGTGAGCCAAT
GCGCGAAGTTTGTTGACGGTGGGTTAGGGAATATCTCGCATTTCGACACT
ATTTAGGAATAGCCTATATAGATAGTGGTCAAAAATTTCCTGATGAGCCG
CTATTTTTGGAGGTGATTTTGATGAATATGATATCGACGATGAACAAGTT
GGCCAACTATTAGGAGGTGAAAGCCCTTATTACGAGAACATTCAGGATGA
ACAATTTGATATAGATATAGGTGACGAGTTATCTGATTGACATTTATTTA
ATAAATTTGTACAAAATATTATGATTTGCATATTTTTTATTAGTTGCATA
TTTTTTTATTGTATTCTAGTTTAAACACTTTATTTTGGGTAAATAATATT
TTAATAAAAAAAGGTTTCATTTAAAAATACCTATACAGTTGTTTAATAAT
TATTTTAAATCCGTTAATATTATTATCATTTTATATTAACATCGATCAGA
ATGTGGCGAGCGTGAAAAAACGTAAGATGGAAAATATTAACCGATTTATT
TTGAAAAACTATTTTACCGTCTTCGATAATAAAAATGTTTAAGAAGATAT
TTTTTGTTAGATGATCCAGCGCCTAATCGAGTATTACCGATAATGCCACA
CAATCAACTCTTACCTAGTGGATCTAAGAAGAAACGACAGAGAAGACAGT
ATTGATTGTGCGAGATCGGA
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protein sequence of SMED30033178-orf-1

>SMED30033178-orf-1 ID=SMED30033178-orf-1|Name=SMED30033178-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
MDAIKDISNELRKLRKENTSLHQQCIQLSRELQRTRATWVEPSRAKKLYQ
RLTAAQKGWQEEKTLNQTQSTNLWIGSCRRSQPRGECGHLPIGVCTRASS
LPGTRPD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron