SMED30027137

Overview
NameSMED30027137
Smed IDSMED30027137
Length (bp)1130
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 SMED30027137 (SMED30027137) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027137 (SMED30027137) 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 SMED30027137 (SMED30027137) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027137 (SMED30027137) 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



SMED30027137

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
epidermisSMED30027137 dd_Smed_v4_13786_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30027137 dd_Smed_v4_13786_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
SMED30027137 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.013176:6020..7122 +5105
Homology
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BLAST of SMED30027137 vs. Planmine SMEST
Match: SMESG000033974.1 (SMESG000033974.1)

HSP 1 Score: 142.124 bits (357), Expect = 5.991e-66
Identity = 70/104 (67.31%), Postives = 81/104 (77.88%), Query Frame = 1 
Query:  274 MKGTWCFPEFTRELYKKITLISRACDDLIIKNRSQGITIADQSATLRQMFTEKELQARLPGRNMAQHLNIIPAHHLTVDSSNYAERDISNIVT-TPTSSTPNRK 582
            MKGTWC PE T++LYKKIT +SRA DDLI+KNRSQ ITIADQ ATLRQ+FTEKELQARLP R++ Q LN+IP  HL V+ SN  E D +N+ T  P  S PNRK
Sbjct:    1 MKGTWCSPEATKKLYKKITRVSRARDDLIVKNRSQRITIADQCATLRQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPNRK 104

HSP 2 Score: 128.642 bits (322), Expect = 5.991e-66
Identity = 74/138 (53.62%), Postives = 91/138 (65.94%), Query Frame = 2 
Query:  617 EKAALQANLSAMENSN*SRMSEVTSHKPICQPDDSDLDVIYTPRLMNLFQPAQTPSQFNISMNSLPTDGPTNVQITISTRKSPFMEKVHEISSGRSTLQIISVTEPP-VRNNFDLAATNVSRQHST*FYEGPGRDVFR 1027
            E A LQ NL  +EN N  ++ EVTS++    P +SDL++I  PRLM+  Q A  P QFNISM +L TD  TN QI IS R SP  E+ HE SSGRST QIISVTEPP VRN+ +  A + SRQ+ T F+   G+D FR
Sbjct:  120 ENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQTQFHRDLGKDTFR 257
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BLAST of SMED30027137 vs. Planmine SMEST
Match: SMESG000021652.1 (SMESG000021652.1)

HSP 1 Score: 187.193 bits (474), Expect = 1.302e-58
Identity = 97/125 (77.60%), Postives = 102/125 (81.60%), Query Frame = 1 
Query:  193 APSVVTTAQYLANLENEHCILKEKYDKMKGTWCFPEFTRELYKKITLISRACDDLIIKNRSQGITIADQSATLRQMFTEKELQARLPGRNMAQHLNIIPAHHLTVDSSNYAERDISNIV-TTPTS 564
            AP VVT AQ+L NLENE  ILKEKY KMKG W   E T ELYKKIT ISRA DDLII+NRSQ ITIADQSA LRQ FTEKELQARLPGRN AQ LN IPA+HL VDSSNYAE ++SNIV TTPTS
Sbjct:   12 APLVVTAAQHLPNLENEQRILKEKYAKMKGIWLSKEATSELYKKITRISRAHDDLIIENRSQRITIADQSAALRQTFTEKELQARLPGRNTAQPLNSIPAYHLLVDSSNYAEHEVSNIVTTTPTS 136
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BLAST of SMED30027137 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 144.05 bits (362), Expect = 3.372e-51
Identity = 72/129 (55.81%), Postives = 90/129 (69.77%), Query Frame = 1 
Query:  187 SLAPSVVTTAQYLANLENEHCILKEKYDKMKGTWCFPEFTRELYKKITLISRACDDLIIKNRSQGITIADQSATLRQMFTEKELQARLPGRNMAQHLNIIPAHHLTVDSSNYAERDISNI---VTTPTS 564
            S APS V  AQYL  LE E+  L+EKY+++K TWC PE TRE YKKI  +SRA DDLII+NRSQ I I+ + A  RQ+FTEKE QARLP RNM Q L+IIP HHL  +  N  + +  N+   +TTP++
Sbjct:   10 SPAPSAVAEAQYLEKLERENFTLREKYNRLKVTWCSPEITRERYKKINRLSRARDDLIIENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPST 138

HSP 2 Score: 77.411 bits (189), Expect = 3.372e-51
Identity = 56/150 (37.33%), Postives = 82/150 (54.67%), Query Frame = 2 
Query:  611 RKEKAALQANLSAMENSN*SRMSEVTSHKPICQPDDSDLDVIYTPRLMNLFQPAQTPSQFNISMNSLPTDGPTNVQITISTRKSPFMEKVHEISSGRSTLQIISVTEPPVRNNFDLAATNVSRQHST*FYEGPGRDVFR*TSMPKKIDEE 1060
            + E A LQ+NL   EN++   ++E+   +PI   D  DL VI  PR  +  QPA  P+Q NI+M++   +   N+QI+I++R +P  +    ISSGRS+ QIISV EP +  N    + N+ R  S+     P R       +P  IDEE
Sbjct:  156 KAENALLQSNLGVRENASLESITELFWPQPIALNDGEDLGVIDAPRQPDFSQPAPIPAQINITMDNYSAEMLINMQISIASRTTPDRDA---ISSGRSSPQIISVIEPTI--NRSQRSDNLPRAPSSSTTRPPKRKY-----LPVDIDEE 295
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BLAST of SMED30027137 vs. Planmine SMEST
Match: SMESG000062943.1 (SMESG000062943.1)

HSP 1 Score: 154.066 bits (388), Expect = 9.734e-46
Identity = 75/117 (64.10%), Postives = 88/117 (75.21%), Query Frame = 1 
Query:  193 APSVVTTAQYLANLENEHCILKEKYDKMKGTWCFPEFTRELYKKITLISRACDDLIIKNRSQGITIADQSATLRQMFTEKELQARLPGRNMAQHLNIIPAHHLTVDSSNYAERDISN 543
            APS V  AQY   L+ E+  L+EKY+K+K TWC PE T+EL KKIT +SRA DDLIIKNR Q ITI+DQSA LRQ+FTEKELQARLP RNM Q L+IIPAHHL  +S    E + +N
Sbjct:   12 APSTVAAAQYAEKLKRENFTLREKYNKLKCTWCSPEATKELIKKITWLSRARDDLIIKNRGQRITISDQSAALRQIFTEKELQARLPSRNMTQRLDIIPAHHLPANSEGSKENNETN 128
[Close]
BLAST of SMED30027137 vs. Planmine SMEST
Match: SMESG000037309.1 (SMESG000037309.1)

HSP 1 Score: 151.369 bits (381), Expect = 2.728e-44
Identity = 84/133 (63.16%), Postives = 96/133 (72.18%), Query Frame = 1 
Query:  187 SLAPSVVTTAQYLANLENEHCILKEKYDKMKGTWCFPEFTRELYKKITLISRACDDLIIKNRSQGITIADQSATLRQMFTEKELQARLPGRNMAQHLNIIPAHHLTVDSSNYAERDISNIVTT-PTSSTPNRK 582
            S AP+V+   Q+LANLENEH ILKEKYDKMKGTW  PE TRELYK IT ISRA DDLI +NRSQ ITIADQSA LRQ+FTEK  +    G  +    NIIP HHL V+SSN+    ++N+VT  PT S  NRK
Sbjct:   10 SPAPAVIAAVQHLANLENEHRILKEKYDKMKGTWRSPEATRELYKNITRISRARDDLIFENRSQRITIADQSAALRQIFTEKSCRC---GYRVEVWPNIIPTHHLPVNSSNH----VTNVVTIEPTPSILNRK 135
The following BLAST results are available for this feature:
BLAST of SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 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 SMED30027137 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000033974.15.991e-6667.31SMESG000033974.1[more]
SMESG000021652.11.302e-5877.60SMESG000021652.1[more]
SMESG000046646.13.372e-5155.81SMESG000046646.1[more]
SMESG000062943.19.734e-4664.10SMESG000062943.1[more]
SMESG000037309.12.728e-4463.16SMESG000037309.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027137 ID=SMED30027137|Name=SMED30027137|organism=Schmidtea mediterranea sexual|type=transcript|length=1130bp
TAAAAACCATTTTCTTCACTCACGTCGTAGTAAATTCAAGTTAAATTCGG
AAGTCTCTTGGATAATAAATTTTGATTCTATTCACTACTAATAACGGCAA
ACTACTCAAACTTATCTAAAAACCTCTATTATTTAGAAAAACCAAATTTC
ACTTACAAACTATGCATCTGCCAAGAATTCCAAGAATCACTGGCTCCGTC
GGTCGTCACTACCGCTCAGTACTTGGCAAATCTAGAAAACGAGCATTGTA
TCCTCAAGGAAAAATATGATAAGATGAAAGGGACATGGTGTTTCCCGGAG
TTCACGAGAGAGTTATATAAAAAGATTACGCTGATTTCCCGAGCCTGTGA
TGACTTAATAATTAAAAACAGAAGTCAAGGGATCACTATTGCGGATCAGA
GTGCTACCCTGAGACAAATGTTTACAGAAAAGGAGCTGCAGGCGCGACTA
CCAGGTCGGAATATGGCCCAACATCTCAATATCATCCCGGCGCACCATCT
GACGGTCGATTCGTCAAATTACGCAGAACGTGACATCTCTAATATTGTCA
CAACGCCAACTTCGTCGACCCCGAATCGTAAATAGAACCTAACAAGAACC
GTCGGAGAAGAGAAAAGAGAAGGCCGCATTACAGGCAAATTTGAGCGCCA
TGGAAAATAGCAATTAGAGTAGGATGTCTGAAGTAACTTCGCACAAGCCT
ATTTGCCAACCCGACGACTCTGATCTGGATGTAATTTACACACCCAGATT
GATGAACCTTTTCCAGCCGGCTCAGACACCGTCTCAATTTAATATCTCGA
TGAATAGCCTCCCCACGGATGGACCAACCAATGTGCAAATAACGATATCC
ACTAGAAAATCTCCTTTCATGGAAAAAGTACACGAAATCTCCAGTGGAAG
ATCCACTCTGCAAATTATTTCGGTCACCGAACCACCGGTACGCAATAATT
TCGACCTGGCAGCTACAAATGTTTCTCGACAACATTCAACCTAATTCTAC
GAAGGCCCAGGAAGAGATGTCTTCCGGTAGACATCGATGCCGAAGAAGAT
TGATGAAGAAATATGATTTTAATGATAATATTTATTTTCATCGTGATTAA
ATTGTAGTTTTAGTTTTTTTTGATCTGTAC
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protein sequence of SMED30027137-orf-1

>SMED30027137-orf-1 ID=SMED30027137-orf-1|Name=SMED30027137-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp
MSEVTSHKPICQPDDSDLDVIYTPRLMNLFQPAQTPSQFNISMNSLPTDG
PTNVQITISTRKSPFMEKVHEISSGRSTLQIISVTEPPVRNNFDLAATNV
SRQHST*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell