SMED30016866

Overview
NameSMED30016866
Smed IDSMED30016866
Length (bp)1422
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 SMED30016866 (SMED30016866) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016866 (SMED30016866) 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 SMED30016866 (SMED30016866) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016866 (SMED30016866) 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



SMED30016866

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30016866 dd_Smed_v4_20214_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30016866 dd_Smed_v4_20214_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30016866 Contig28235newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
early male germ cellSMED30016866 H_55_10a_-2GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30016866 vs. Planmine SMEST
Match: SMESG000005768.1 (SMESG000005768.1)

HSP 1 Score: 172.555 bits (436), Expect = 4.316e-52
Identity = 88/132 (66.67%), Postives = 104/132 (78.79%), Query Frame = 1 
Query:  637 ICGKSHPFRKEDSTCASYKEKCENPKSEECKQLTLQCDQCPIKESKDANDRWRQSM-------RQMIQTLLEKKNERSEIEHENLSMRKILDTIIRKIQKITETNPEYKQMQEILRDVRSIKRQSPNKSQQV 1011
            +CGK HPFRKEDSTC +YKE CENPK EEC+QL LQC+Q P K  ++ ND+ +QS+       RQMIQTLL+ KNERS+IE+ENL M+K LD I RKIQ+I ETNPE +QMQEILR +RSIKRQS NKSQQ 
Sbjct:    1 MCGKLHPFRKEDSTCLNYKEICENPKGEECQQLALQCNQFPTKRGENVNDKLKQSIEKESQRIRQMIQTLLDTKNERSKIENENLDMKKSLDIIGRKIQRIPETNPENEQMQEILRAIRSIKRQSSNKSQQT 132
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BLAST of SMED30016866 vs. Planmine SMEST
Match: SMESG000012882.1 (SMESG000012882.1)

HSP 1 Score: 160.614 bits (405), Expect = 6.147e-42
Identity = 96/151 (63.58%), Postives = 129/151 (85.43%), Query Frame = 2 
Query:    2 LKRELARIKTQVILEDYWKTEAERLRKSRKSEQQYLIQLEETCNKAREIKQNHQQAQEEIEXXXXXXXXXXXXXXXXXXXXXXXXXXLERKQKTERNLRVQLNHQRKILNKNKEQLEELPKLTERLVKTQILIMRFSEARAKEECIMHSPP 454
            LKRELA IKT+VILEDYWKTEAER+R SRKSEQ+Y+IQLE +C +AREIK++HQQAQEEI+ L  +LQ+ K+K +KQ T +++YK +L+RKQ  ERNL++++++Q++I+ + KE+L+ELPKLTERL+K Q+LIMRFSE + KEEC  HS P
Sbjct: 3586 LKRELAEIKTRVILEDYWKTEAERMRDSRKSEQRYVIQLENSCKEAREIKESHQQAQEEIKTLTDQLQEAKRKLEKQTTKRVNYKRQLKRKQTKERNLQMKIHNQQRIIKEGKERLKELPKLTERLIKAQVLIMRFSENKIKEECERHSTP 3736
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BLAST of SMED30016866 vs. Planmine SMEST
Match: SMESG000053822.1 (SMESG000053822.1)

HSP 1 Score: 160.229 bits (404), Expect = 8.463e-42
Identity = 93/151 (61.59%), Postives = 130/151 (86.09%), Query Frame = 2 
Query:    2 LKRELARIKTQVILEDYWKTEAERLRKSRKSEQQYLIQLEETCNKAREIKQNHQQAQEEIEXXXXXXXXXXXXXXXXXXXXXXXXXXLERKQKTERNLRVQLNHQRKILNKNKEQLEELPKLTERLVKTQILIMRFSEARAKEECIMHSPP 454
            L+RELA IKT+VILEDYWKTEAER+R SRKSEQ+Y+IQLE++C +AREIK++HQQAQ+EI+ L  +LQ+ ++K +KQ T +++YK +L+RKQ  ERNL++++++Q++I+ +NKE+L+ELPKLTERL+K Q+LIMRFSE + KEEC  H  P
Sbjct: 5645 LRRELAEIKTRVILEDYWKTEAERMRDSRKSEQRYVIQLEDSCKEAREIKESHQQAQDEIKTLTEQLQEARRKLEKQTTKRVNYKRQLKRKQAKERNLQMKIHNQQRIIKENKERLKELPKLTERLIKAQVLIMRFSENKTKEECEKHPTP 5795
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BLAST of SMED30016866 vs. Planmine SMEST
Match: SMESG000004687.1 (SMESG000004687.1)

HSP 1 Score: 154.066 bits (388), Expect = 8.166e-40
Identity = 91/151 (60.26%), Postives = 130/151 (86.09%), Query Frame = 2 
Query:    2 LKRELARIKTQVILEDYWKTEAERLRKSRKSEQQYLIQLEETCNKAREIKQNHQQAQEEIEXXXXXXXXXXXXXXXXXXXXXXXXXXLERKQKTERNLRVQLNHQRKILNKNKEQLEELPKLTERLVKTQILIMRFSEARAKEECIMHSPP 454
            L+RELA IKT+VILE+YWKTEAER+R SRKSEQ+Y++QLE++C +AR+IK++HQQAQ+EI+ L  +LQ+ K+K +KQ T +++YK +L+RKQ  ERNL++++ +Q++I+ +NKE+L+ELPK+TERL++ QILIMRFSE + KEEC  HS P
Sbjct:   87 LRRELAEIKTRVILENYWKTEAERMRDSRKSEQRYVLQLEDSCKEARKIKESHQQAQDEIKTLTEQLQEAKRKLEKQTTKRVNYKRQLKRKQTKERNLQMKICNQQRIIKENKERLKELPKITERLIRAQILIMRFSENKIKEECERHSTP 237

HSP 2 Score: 153.295 bits (386), Expect = 1.267e-39
Identity = 100/227 (44.05%), Postives = 142/227 (62.56%), Query Frame = 1 
Query:  613 CVTENPLDICGKSHPFRKEDSTCASYKEKCENPKSEECKQLTLQCDQCPIKESKDANDRWRQSMRQMIQTLLEKKNERSEIEHENLSMRKILDTIIRKIQKITETNPEYKQMQEILRDVRSIKRQSPNKSQQVYESNLTTPQIQIVT-ISLILNIMSXXXXXXXXXXXXNQPRQNTSTQKNQELTSQIRNPKRSQEIERLSYISINKPSQSKPTREEYHLEAETNAI 1290
            C TENPL+ C KS PFRKEDSTCA YKE C NP +EEC+Q+ LQC QCP+KE+KD   +  +  + M+QTLL+   E + I++EN   +K L+T+IR+IQ+  + NP  K +QEI +   SI++Q   +  Q  E   TT  I+++  IS+  NI+ L  C +      N+ RQNT  QK + + +QIRN  +  +  +LS+ISIN PS+S        LE+ET A+
Sbjct:  244 CDTENPLEKCEKSQPFRKEDSTCADYKEICSNPDNEECQQINLQCIQCPMKENKDEIKQNIEKTQIMVQTLLKNNEEIANIKNENRETKKTLETLIRQIQRKAKANPNNKPIQEIQKITLSIQKQLGKRVGQENEPRTTTLSIELILPISITSNII-LFICCLILGLTKNKQRQNTPIQKFRRMINQIRNTNQISKTAKLSHISINHPSRST------QLESETQAV 463
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BLAST of SMED30016866 vs. Planmine SMEST
Match: SMESG000074160.1 (SMESG000074160.1)

HSP 1 Score: 152.91 bits (385), Expect = 2.319e-39
Identity = 87/144 (60.42%), Postives = 124/144 (86.11%), Query Frame = 2 
Query:    2 LKRELARIKTQVILEDYWKTEAERLRKSRKSEQQYLIQLEETCNKAREIKQNHQQAQEEIEXXXXXXXXXXXXXXXXXXXXXXXXXXLERKQKTERNLRVQLNHQRKILNKNKEQLEELPKLTERLVKTQILIMRFSEARAKEE 433
            L+RELA IKT+VILEDYWKTEAER+R SRKSEQ+Y+IQLE++C +AREIK+NHQQAQ+EI+ L  +LQ+ ++K +KQ   +++ K +L+RKQ  ERNL++++ +Q++++ +NKE+L+ELPK+TERL+K Q+LIMRFSE + KEE
Sbjct: 5630 LRRELAEIKTRVILEDYWKTEAERMRDSRKSEQRYVIQLEDSCKEAREIKENHQQAQDEIKALTEQLQEARRKLEKQTAKRINSKRQLKRKQTKERNLQMKIYNQQRVIKENKERLKELPKITERLIKAQVLIMRFSENKTKEE 5773

HSP 2 Score: 126.331 bits (316), Expect = 1.986e-30
Identity = 89/222 (40.09%), Postives = 132/222 (59.46%), Query Frame = 1 
Query:  664 KEDSTCASYKEKCENPKSEECKQLTLQCDQCPIKESKDANDRWRQSMRQMIQTLLEKKNERSEIEHENLSMRKILDTIIRKIQKITETNPEYKQMQEILRDVRSIKRQSPNKSQQVYESNLTTPQIQIVTISLILNIMSXXXXXXXXXXXXNQPRQNTSTQKNQELTSQIRNPKRSQEIERLSYISINKPSQSKPTREEYHLEAETNAIIKDNRDSFETKFD 1329
            +EDSTCA YKE C NP +EEC+Q+ LQC QCP KE+KD   +  +  + M+QTLL+   E + I++EN  ++K L+T+IR+IQ+  + NP  K +QEI     SIKRQ   + +   E + T+  I+++    I + M L+ C +      N+ RQNT  QK + + + I+N  +  +  RLS ISIN PS+S        LE+ET A+     DSFE K++
Sbjct: 5774 REDSTCADYKEMCSNPNNEECQQINLQCMQCPTKENKDELKQNIERTQAMVQTLLKNNEEIANIKNENREIKKTLETLIRQIQRKAKANPNNKPIQEI---ALSIKRQQGKQIKN--EPSTTSLSIELILPISITSNMILLICCLILGLTKNKQRQNTPIQKLRRMFNPIQNTNQVSKTSRLSQISINHPSRST------QLESETQAV----SDSFEAKYN 5980
The following BLAST results are available for this feature:
BLAST of SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 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 SMED30016866 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000005768.14.316e-5266.67SMESG000005768.1[more]
SMESG000012882.16.147e-4263.58SMESG000012882.1[more]
SMESG000053822.18.463e-4261.59SMESG000053822.1[more]
SMESG000004687.18.166e-4060.26SMESG000004687.1[more]
SMESG000074160.12.319e-3960.42SMESG000074160.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016866 ID=SMED30016866|Name=SMED30016866|organism=Schmidtea mediterranea sexual|type=transcript|length=1422bp
CCTAAAGCGAGAGTTAGCGAGAATAAAAACCCAAGTAATCCTCGAAGATT
ATTGGAAAACGGAAGCAGAAAGATTGAGAAAAAGCAGAAAAAGCGAACAA
CAATACCTAATCCAATTGGAAGAAACCTGTAACAAAGCAAGGGAAATTAA
ACAGAACCACCAACAAGCCCAAGAGGAAATCGAAATGTTAAAAGGAAAGT
TACAGAAACAAAAACAGAAAACCAAGAAACAGAAAACTAGTAAAATGAGC
TACAAATATAAACTCGAGAGAAAACAGAAGACTGAGAGAAACCTAAGAGT
GCAATTAAACCACCAACGAAAGATACTCAATAAAAACAAAGAACAACTAG
AAGAGCTTCCAAAACTGACAGAACGATTAGTAAAGACACAAATATTGATA
ATGAGATTCTCCGAAGCAAGGGCGAAAGAGGAATGTATAATGCACTCACC
ACCGGGTGAGCAGGGAGAATAACGAGATCCTAAATAAAGCGCAAATCTAC
TGTATATAGACAAAACATGTAAATAGTCTTCAAGTAACCAATGTATAATA
GAATGAGAACTGAAGCAAATCTAAAGAAACTGTATATGATGATGATGGTA
ACAATAAAGCTATGTGTAACCGAAAACCCCTTAGATATATGCGGAAAATC
TCACCCATTCCGAAAAGAAGATAGTACGTGTGCAAGCTACAAGGAAAAAT
GTGAAAACCCAAAGAGCGAAGAATGCAAACAATTAACCCTACAATGTGAT
CAATGCCCAATAAAAGAAAGCAAAGATGCCAACGACAGATGGAGACAAAG
TATGAGACAAATGATACAAACCTTATTAGAGAAAAAGAATGAGAGATCCG
AAATAGAACATGAAAACCTGAGTATGAGGAAAATCCTAGATACTATCATC
AGAAAAATCCAAAAGATCACTGAAACGAACCCAGAATATAAGCAAATGCA
AGAAATCCTAAGAGATGTCCGTTCAATCAAAAGACAGTCACCAAATAAAT
CCCAACAAGTATACGAATCAAACCTAACGACACCACAAATTCAAATCGTA
ACGATCAGTCTAATCTTAAACATTATGTCATTGATATGCTGTCTTATAAC
CTGTCTGAGAATAATCAATCAACCAAGACAGAACACCTCAACTCAGAAAA
ACCAAGAATTAACCAGTCAAATTCGTAATCCCAAAAGAAGCCAAGAAATA
GAAAGACTCTCGTATATATCGATAAATAAGCCAAGCCAATCCAAGCCAAC
AAGAGAAGAATATCACTTAGAAGCAGAAACCAACGCCATCATCAAAGACA
ATCGCGATTCATTTGAGACTAAATTTGATAATCACTGAATAACTGTGTAT
TAACGTAACTAAAAAACTGAAACTGATTTGACTTCAATTTGATTTTTATA
TATAGTAGTCGGACTATAAGTC
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protein sequence of SMED30016866-orf-1

>SMED30016866-orf-1 ID=SMED30016866-orf-1|Name=SMED30016866-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=157bp
LKRELARIKTQVILEDYWKTEAERLRKSRKSEQQYLIQLEETCNKAREIK
QNHQQAQEEIEMLKGKLQKQKQKTKKQKTSKMSYKYKLERKQKTERNLRV
QLNHQRKILNKNKEQLEELPKLTERLVKTQILIMRFSEARAKEECIMHSP
PGEQGE*
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protein sequence of SMED30016866-orf-2

>SMED30016866-orf-2 ID=SMED30016866-orf-2|Name=SMED30016866-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=266bp
MYNRMRTEANLKKLYMMMMVTIKLCVTENPLDICGKSHPFRKEDSTCASY
KEKCENPKSEECKQLTLQCDQCPIKESKDANDRWRQSMRQMIQTLLEKKN
ERSEIEHENLSMRKILDTIIRKIQKITETNPEYKQMQEILRDVRSIKRQS
PNKSQQVYESNLTTPQIQIVTISLILNIMSLICCLITCLRIINQPRQNTS
TQKNQELTSQIRNPKRSQEIERLSYISINKPSQSKPTREEYHLEAETNAI
IKDNRDSFETKFDNH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0002030early male germ cell
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 88..108
NoneNo IPR availableTMHMMTMhelixcoord: 167..189