SMED30029783

Overview
NameSMED30029783
Smed IDSMED30029783
Length (bp)1237
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 SMED30029783 (SMED30029783) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029783 (SMED30029783) 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.
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




SMED30029783

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30029783 SmedASXL_076775SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
parenchymaSMED30029783 dd_Smed_v4_17283_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
BLAST of SMED30029783 vs. TrEMBL
Match: A0A0C2MSD4 (Uncharacterized protein OS=Thelohanellus kitauei OX=669202 GN=RF11_16157 PE=4 SV=1)

HSP 1 Score: 115.161 bits (287), Expect = 1.018e-25
Identity = 67/158 (42.41%), Postives = 94/158 (59.49%), Query Frame = 2
Query:  380 VADKDVELAQCSRILDQKKLAENINAQLTFEETEIRNLSIR-Q*NEREMIHGVREYVVE*ICTEKLLHLVHDLHSIPISPNECDESDYHSN------KSFIDNQNSFIAVIHQFNGTTIHMLRSFKYVYLWLLRGRYSAVDTNSKERNLDYLSDENWK 832
            + ++D ELAQ +RILDQK+ +EN+  Q+TF E EIR LS R Q NEREMI G REY  +    E LL L+   H+I IS +EC+      N      ++ +  +   + +  +  G  +      KYV  WLLR R+SAVD+ S++RN D+LSDEN +
Sbjct:   98 LTNEDAELAQWARILDQKQWSENVTNQITFGEMEIRKLSNRLQLNEREMIRGFREYFTKKTYPETLLLLIRATHTISISSSECERGFSQMNLIIPPIRASLMTKTVSLLIFIRLVGPPLTFFDPSKYVDSWLLRRRHSAVDSQSRKRNRDHLSDENMR 255          
BLAST of SMED30029783 vs. TrEMBL
Match: A0A1B6M310 (Uncharacterized protein (Fragment) OS=Graphocephala atropunctata OX=36148 GN=g.1297 PE=4 SV=1)

HSP 1 Score: 75.8702 bits (185), Expect = 6.416e-12
Identity = 49/154 (31.82%), Postives = 82/154 (53.25%), Query Frame = 2
Query:  386 DKDVELAQCSRILDQKKLAENINAQLTFEETEIRNLSIR-Q*NEREMIHGVREYVVE*ICTEKLLHLVHDLHSIPISPNECDESDYHSNKSFIDNQNSF-IAVIH-----QFNGTTIHMLRSFKYVYLWLLRGRYSAVDTNSKERNLDYLSDEN 826
            +KD +LA+  +++D +   E+I   +TF E E+R L+ R + NER++I G REY+      + L  L   ++S+ IS +EC+      N      ++S  I  +      + NG  + + +  KYV  WL+ G +SA+   SKER+ +   DEN
Sbjct:   88 EKDTKLAETFKVMDTRNWPEDI--PITFGENEMRELASRFKLNERQLITGFREYIYSRTLPDSLCRLEQSINSVAISSSECERGFSQMNLIITPLRSSLKITTVSGLLFVKINGPPLRLFQPEKYVDTWLVSGHHSALAVKSKERSREKKYDEN 239          
BLAST of SMED30029783 vs. TrEMBL
Match: A0A0C2MTG0 (Uncharacterized protein OS=Thelohanellus kitauei OX=669202 GN=RF11_11350 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 6.819e-12
Identity = 50/126 (39.68%), Postives = 68/126 (53.97%), Query Frame = 2
Query:  479 EIRNLSIR-Q*NEREMIHGVREYVVE*ICTEKLLHLVHDLHSIPISPNECDESDYHSNKSFIDNQNSFIA------VIHQFNGTTIHMLRSFKYVYLWLLRGRYSAVDTNSKERNLDYLSDENWKN 835
            EIR LS R Q NEREMI G  EY++E    E LL L+  + +I IS ++C+      N      + S +       +  +  G  +      KYV  WLLRGR+SAVD+ S++RN D LSDEN + 
Sbjct:    2 EIRKLSNRLQLNEREMIRGFCEYLMEKTSGETLLLLIRGILTICISSSKCERGFSLMNLIMTLTRASLMTETVSSLIFIRLVGPPLTFFDPSKYVDSWLLRGRHSAVDSQSRKRNRD-LSDENMRK 126          
BLAST of SMED30029783 vs. TrEMBL
Match: A0A0C2MWK9 (Uncharacterized protein OS=Thelohanellus kitauei OX=669202 GN=RF11_15812 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 5.861e-11
Identity = 46/92 (50.00%), Postives = 59/92 (64.13%), Query Frame = 3
Query:  489 TCQ*DNKMKE-----K*FMESVNTL*NKYVLKN---YFI*YTIYILSPFLQMNV--MNLIIIPTRASLITKTVSSLLFISLTGPPFTCFDPS 734
            TC  D++ K+     K F++SVNTL  +++ K+    F+ YTI I S   +     MNLII P RASL+TKTVSSL+FI L GPP T FDPS
Sbjct:  102 TCYGDDRKKQLTSLRKKFVDSVNTLWKRHIQKHCFCLFVLYTISISSSECERGFSQMNLIIPPIRASLMTKTVSSLIFIRLVGPPLTFFDPS 193          
BLAST of SMED30029783 vs. Planmine SMEST
Match: SMESG000045502.1 (SMESG000045502.1)

HSP 1 Score: 62.003 bits (149), Expect = 1.906e-10
Identity = 36/78 (46.15%), Postives = 48/78 (61.54%), Query Frame = 2
Query:  380 VADKDVELAQCSRILDQKKLAENINAQLTFEETEIRNLSIR-Q*NEREMIHGVREYVVE*ICTEKLLHLVHDLHSIPI 610
            +++KD +LA  +R+LD K   +NI   L F + EIRNLS R Q NE  MI G REY+ E    +KLL L    ++IPI
Sbjct:   84 LSNKDADLAYSARVLDLKHWPDNIYTHLAFGDEEIRNLSTRLQLNETTMIRGFREYLTEKNVPDKLLPLQTAHNTIPI 161          
The following BLAST results are available for this feature:
BLAST of SMED30029783 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 SMED30029783 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 SMED30029783 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 SMED30029783 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 SMED30029783 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 SMED30029783 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 SMED30029783 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 SMED30029783 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A0C2MSD41.018e-2542.41Uncharacterized protein OS=Thelohanellus kitauei O... [more]
A0A1B6M3106.416e-1231.82Uncharacterized protein (Fragment) OS=Graphocephal... [more]
A0A0C2MTG06.819e-1239.68Uncharacterized protein OS=Thelohanellus kitauei O... [more]
A0A0C2MWK95.861e-1150.00Uncharacterized protein OS=Thelohanellus kitauei O... [more]
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BLAST of SMED30029783 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 SMED30029783 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 SMED30029783 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 SMED30029783 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 SMED30029783 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 SMED30029783 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000045502.11.906e-1046.15SMESG000045502.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029783 ID=SMED30029783|Name=SMED30029783|organism=Schmidtea mediterranea sexual|type=transcript|length=1237bp
ACTTCCATAATAATCAACGTATTCCTTCAAATTAAAATTAATAATAGTTA
AAATTAAAATAATTCAAAAGTAACTGACGTAACACAAAAAAATATTTCCA
TTTTGTTAGGATTCTAAATTTTTGATTATTTACAAACTTACTGATTCACA
CTAGTAACCAGTTCTTTTTTCTGACATAATGTGACGGAACTACGTTCCGG
CACCTTTTTTCGTTACGACTTAAAATATAATTTGCAGAAGTTACATTTTT
TGTGTTTTTTGTCGTATTATAAAAGATATGCAAATATATCAATTACAAAT
GGNGCCCAGTAAATTTTCGCTGGCTGAACTATCCAACGTATGTCTATGCC
AGCGAACTTTGTGCTTACTCTGAGAAAAGGTTGCTGACAAAGACGTTGAA
TTAGCTCAGTGTTCCCGCATCTTAGACCAAAAGAAATTGGCAGAAAACAT
TAACGCTCAGCTGACATTTGAAGAAACTGAAATAAGAAACTTGTCAATAA
GACAATAAAATGAAAGAGAAATGATTCATGGAGTCCGTGAATACGTTGTA
GAATAAATATGTACTGAAAAACTACTTCATTTAGTACACGATCTACATTC
TATCCCCATTTCTCCAAATGAATGTGATGAATCTGATTATCATTCCAACA
AGAGCTTCATTGATAACCAAAACAGTTTCATCGCTGTTATTCATCAGTTT
AACGGGACCACCATTCACATGCTTCGATCCTTCAAGTACGTTTATTTGTG
GTTACTTCGGGGAAGATATTCAGCTGTAGACACTAATAGCAAGGAAAGAA
ATCTAGACTATTTGTCTGACGAAAATTGGAAAAACTATGGGATTTGTTAT
AAAGGTGAATTTTTACATATAAATACAAAAACACATGTGTTCCAGCTCCT
TTTTCCCACACAAAAGCACTGCTAGTAATGAATTCTAAAATGATGCTTAA
TAAATAATTGTTTAAATAATACAATATTTTCATATTAAAAACCCGGGTGC
TTTTATTGACATTTTTTCTGACGACGCTTCTATTATATATTTAAAATTCT
TCAAATAGATAAGTTAAACCTTTAACTGAATAATATAATTTTGGATGGTA
GAAAAAAATCTGNAAACTGTTTAGCTTAAGTTTATATAATACATATTGTA
TTGATCATGTTGTTGCAAATATAATGAAAGAAAATTCTAAAGATGAAAAT
TAATTGATAATCTCCATAAAATATGTTTAAATAGAAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002075pigment cell