SMED30021277

Overview
NameSMED30021277
Smed IDSMED30021277
Length (bp)771
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 SMED30021277 (SMED30021277) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021277 (SMED30021277) 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 SMED30021277 (SMED30021277) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021277 (SMED30021277) 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




SMED30021277

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30021277SMESG000032006.1 Contig2546newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30021277SMESG000032006.1 Contig2546uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30021277SMESG000016731.1 Contig2546newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30021277SMESG000016731.1 Contig2546uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30021277SMESG000032006.1 SmedASXL_009594SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021277 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002415:63506..64269 +3811
Homology
BLAST of SMED30021277 vs. Planmine SMEST
Match: SMESG000032006.1 (SMESG000032006.1)

HSP 1 Score: 374.4 bits (960), Expect = 2.029e-133
Identity = 184/184 (100.00%), Postives = 184/184 (100.00%), Query Frame = 3
Query:   33 MAHLFEKSYESLSEINYQLSTQHSIENEIFDFLENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYLPCGDIVICSECYNDSVVKCQGCQRHVDEMHKIYF 584
            MAHLFEKSYESLSEINYQLSTQHSIENEIFDFLENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYLPCGDIVICSECYNDSVVKCQGCQRHVDEMHKIYF
Sbjct:    1 MAHLFEKSYESLSEINYQLSTQHSIENEIFDFLENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYLPCGDIVICSECYNDSVVKCQGCQRHVDEMHKIYF 184          
BLAST of SMED30021277 vs. Planmine SMEST
Match: SMESG000031958.1 (SMESG000031958.1)

HSP 1 Score: 133.65 bits (335), Expect = 1.397e-38
Identity = 67/167 (40.12%), Postives = 97/167 (58.08%), Query Frame = 3
Query:   84 QLSTQHSIENEIFDFLENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYLPCGDIVICSECYNDSVVKCQGCQRHVDEMHKIYF 584
            ++S    ++N + +F  + E  PLK +++ +KS  NE++  L E FGY  S+LKLAS +I  N++    E +N+IFW CM LR DK C KII   M   D I +++  I  K ++  LTC  C    VS+LYLPCG +V CS C+  +   C  C   ++E H IYF
Sbjct:   24 EISLVEIVKNTLLNFQLDLEKWPLKMMRKFIKSLKNEFIFKLSETFGYNPSILKLASWIICFNEMKNDDENLNDIFWICMELRFDKECWKIIDILMRKTDEIEIEINNIVKKQNESLLTCSICMKEQVSVLYLPCGHVVACSRCHQSTFHSCLACGIKIEEFHIIYF 190          
BLAST of SMED30021277 vs. Planmine SMEST
Match: SMESG000067789.1 (SMESG000067789.1)

HSP 1 Score: 120.553 bits (301), Expect = 2.844e-33
Identity = 58/153 (37.91%), Postives = 91/153 (59.48%), Query Frame = 3
Query:  123 DFLENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYLPCGDIVICSECYNDSVVKCQGCQRHVDEMHKIY 581
            DF+  Y+    K +  I+K F N  +E L + F Y++ +LKL+S ++ +++     + +NE FWDCM LRL+    ++ K W+   D I   L +  N + K YLTC  C+ N VS+LYLPCG +++CS+C + +  KCQ C   ++E H IY
Sbjct:   58 DFINTYDTFTDKEIINILKIFKNPSIEYLIDIFNYDKCILKLSSYLMYLDKTGMDNDSLNEYFWDCMELRLNPEYSRLFKEWIRKSDFIEDKLTEKLNDVKKRYLTCSICKENQVSVLYLPCGHVIVCSKCQDKNNRKCQACSAPINEYHAIY 210          
BLAST of SMED30021277 vs. Planmine SMEST
Match: SMESG000031926.1 (SMESG000031926.1)

HSP 1 Score: 117.857 bits (294), Expect = 2.069e-32
Identity = 57/152 (37.50%), Postives = 92/152 (60.53%), Query Frame = 3
Query:  126 FLENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYLPCGDIVICSECYNDSVVKCQGCQRHVDEMHKIY 581
            FL +     L  + ++ KSF +E +E L + FGY  ++LKL+SCVIS+N I  +    N +FW CM  R+ +   K+I+ +M N+D +  ++     + ++ +LTC  C+ N VS+LYLPCG IV+CS C+  +  +C+ C   +DE H +Y
Sbjct:   47 FLSSTNGFDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFNTNLVFWSCMEFRVGQY-QKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCFKSTTRRCESCAVDIDEYHFVY 197          
BLAST of SMED30021277 vs. Planmine SMEST
Match: SMESG000031949.1 (SMESG000031949.1)

HSP 1 Score: 110.153 bits (274), Expect = 1.620e-29
Identity = 51/150 (34.00%), Postives = 90/150 (60.00%), Query Frame = 3
Query:  132 ENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYLPCGDIVICSECYNDSVVKCQGCQRHVDEMHKIY 581
            +++E L    + +++KSF    ++  H+ FGY++ +LKL S +++  +I  + + MN +FW CM LRLD      I  W+ N +++ L  ++    ++  YL C  C++  VSILYLPCG +++C++C+  +   CQ CQ  ++E H IY
Sbjct:   43 DSFENLDFIFLGKLLKSFNEPLIQYFHDTFGYDKPLLKLVSFILNSYEIKVNKDNMNFLFWTCMELRLDFEYRSEINKWISNFEQLKLKAQEKFQNIASFYLKCFLCKIQQVSILYLPCGHLILCTKCFQRNTKYCQICQILIEEAHTIY 192          
The following BLAST results are available for this feature:
BLAST of SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 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 SMED30021277 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000032006.12.029e-133100.00SMESG000032006.1[more]
SMESG000031958.11.397e-3840.12SMESG000031958.1[more]
SMESG000067789.12.844e-3337.91SMESG000067789.1[more]
SMESG000031926.12.069e-3237.50SMESG000031926.1[more]
SMESG000031949.11.620e-2934.00SMESG000031949.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021277 ID=SMED30021277|Name=SMED30021277|organism=Schmidtea mediterranea sexual|type=transcript|length=771bp
CAACTCTGCTAAATTACTAATTGTAATAAACAATGGCGCATTTATTTGAG
AAATCATATGAAAGTTTATCGGAAATAAATTATCAACTCTCAACTCAACA
TTCAATTGAAAATGAAATATTTGATTTCCTTGAAAATTACGAAATTCTCC
CACTGAAAACGGTTCAAAGGATTGTCAAATCATTTGCAAATGAATATGTG
GAAATTTTGCATGAAAAGTTTGGATACGAGCAATCGGTTCTGAAACTAGC
AAGCTGCGTCATTTCTATAAATCAAATTGATGAATCTCTGGAACGAATGA
ATGAAATATTCTGGGACTGCATGAATTTGAGATTGGACAAGTCATGCGGA
AAAATCATCAAAAGTTGGATGTTAAATATCGATAGGATTGTGCTTGATTT
GAAGAAAATATCTAACAAATTAAGTAAAGAATATTTAACATGTTGTGCTT
GTCAATTAAATCCAGTGTCCATTTTGTATCTGCCTTGTGGAGACATTGTG
ATCTGTTCAGAATGCTACAATGACTCAGTGGTAAAATGTCAAGGTTGCCA
ACGTCATGTTGACGAGATGCACAAGATTTATTTTTGAATTTTGAAATGGC
GGATTTCTATAAAGGTTTCTATCGATGGTGAAATTGGAAATAAAAGGAAA
TTAATAAAATATTTGTCGAAAAGTATTATCATTTAATTTCATCATTTTAA
AATAAGAAAGAAAACTTTTTCATTTTTACATTTACTATGTGATCAAATAA
AAATTTATCATTTAAAAAAAA
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protein sequence of SMED30021277-orf-1

>SMED30021277-orf-1 ID=SMED30021277-orf-1|Name=SMED30021277-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=185bp
MAHLFEKSYESLSEINYQLSTQHSIENEIFDFLENYEILPLKTVQRIVKS
FANEYVEILHEKFGYEQSVLKLASCVISINQIDESLERMNEIFWDCMNLR
LDKSCGKIIKSWMLNIDRIVLDLKKISNKLSKEYLTCCACQLNPVSILYL
PCGDIVICSECYNDSVVKCQGCQRHVDEMHKIYF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR013083Znf_RING/FYVE/PHD
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 121..184
e-value: 6.1E-8
score: 33.9