SMED30028707

Overview
NameSMED30028707
Smed IDSMED30028707
Length (bp)1848
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 SMED30028707 (SMED30028707) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028707 (SMED30028707) 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 SMED30028707 (SMED30028707) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028707 (SMED30028707) 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




SMED30028707

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30028707 Contig6766newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30028707 Contig6766uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
dorsal ventral margin of the whole animalSMED30028707 Contig6766newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
dorsal ventral margin of the whole animalSMED30028707 Contig6766uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30028707 Contig6766newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30028707 Contig6766uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30028707 vs. Planmine SMEST
Match: SMESG000042929.1 (SMESG000042929.1)

HSP 1 Score: 126.716 bits (317), Expect = 4.928e-55
Identity = 74/103 (71.84%), Postives = 82/103 (79.61%), Query Frame = -1
Query:  634 MEFLLNPDEITKKXXXXXXXXXXXELTPATTAINSTSQISISLADRWRWAWAQHRQEKCPDFPPSKFLYRNNLWMGTSTQWSPTEEIYRQARQQLEDLVAQQR 942
            M+   N ++ T KSGMSSE EASGEL P T   +S  Q  ISLADRWRWAWAQ+RQEKCPDFPPSKFL R+NL  GTSTQWSPTEEIY+QARQQLE L A+QR
Sbjct:    1 MDSYFNSNKSTAKSGMSSEEEASGELVPTTAVTHSIDQTLISLADRWRWAWAQYRQEKCPDFPPSKFLDRDNLGRGTSTQWSPTEEIYQQARQQLESLEARQR 103          

HSP 2 Score: 108.227 bits (269), Expect = 4.928e-55
Identity = 54/72 (75.00%), Postives = 59/72 (81.94%), Query Frame = -2
Query:  444 RNNALQVARARQQIANVKEDLLAGRIADSYWHPHQI-----PSTNAARTRNTKRPTMSISGYTPEEWVASRF 644
            R+  LQV  ARQ +ANV+EDLLAGRIAD+YWH HQI     P TNAAR RNTKRPTMSISG+TPEEWVASRF
Sbjct:  103 RDMDLQVTGARQHLANVEEDLLAGRIADTYWHLHQITPVQTPPTNAARARNTKRPTMSISGFTPEEWVASRF 174          
BLAST of SMED30028707 vs. Planmine SMEST
Match: SMESG000009297.1 (SMESG000009297.1)

HSP 1 Score: 125.946 bits (315), Expect = 1.031e-54
Identity = 75/102 (73.53%), Postives = 84/102 (82.35%), Query Frame = -1
Query:  637 MEFLLNPDEITKKXXXXXXXXXXXELTPATTAINSTSQISISLADRWRWAWAQHRQEKCPDFPPSKFLYRNNLWMGTSTQWSPTEEIYRQARQQLEDLVAQQ 942
            MEF L+ DE T KSGM SEGE SG+L  AT AINST    ISLADRWRWAWAQ+RQE+CPDFPPSKFL R+NL   TSTQWSP+EEIY+QA QQLE+LV+QQ
Sbjct:    1 MEFTLHSDEATIKSGMFSEGEGSGKLVAATIAINST----ISLADRWRWAWAQYRQERCPDFPPSKFLDRDNLGGVTSTQWSPSEEIYQQALQQLENLVSQQ 98          

HSP 2 Score: 107.842 bits (268), Expect = 1.031e-54
Identity = 52/67 (77.61%), Postives = 58/67 (86.57%), Query Frame = -2
Query:  444 QVARARQQIANVKEDLLAGRIADSYWHPHQI-----PSTNAARTRNTKRPTMSISGYTPEEWVASRF 629
            QV RARQ +ANV+E+LLAGRIADSYWHPHQI     P  NAARTRNTKRPTM+ISGYTPEEWVA++F
Sbjct:  104 QVTRARQHLANVEENLLAGRIADSYWHPHQISPDQTPPNNAARTRNTKRPTMAISGYTPEEWVATQF 170          
BLAST of SMED30028707 vs. Planmine SMEST
Match: SMESG000065282.1 (SMESG000065282.1)

HSP 1 Score: 133.265 bits (334), Expect = 1.298e-54
Identity = 76/108 (70.37%), Postives = 87/108 (80.56%), Query Frame = -1
Query:  637 KVYFTIMEFLLNPDEITKKXXXXXXXXXXXELTPATTAINSTSQISISLADRWRWAWAQHRQEKCPDFPPSKFLYRNNLWMGTSTQWSPTEEIYRQARQQLEDLVAQQ 960
            K+ +  MEF L  +E+T KS M S GE SGEL PA+TAINST    ISLADRWRWAWAQ+RQE+CPDFPPSKFL R+NL  G STQWSP EEIY+QARQQLE+LV+QQ
Sbjct:    9 KIDWKFMEFSLASNELTTKSRMPSRGEGSGELAPASTAINST----ISLADRWRWAWAQYRQERCPDFPPSKFLDRDNLGRGMSTQWSPPEEIYQQARQQLENLVSQQ 112          

HSP 2 Score: 100.523 bits (249), Expect = 1.298e-54
Identity = 49/67 (73.13%), Postives = 55/67 (82.09%), Query Frame = -2
Query:  444 QVARARQQIANVKEDLLAGRIADSYWHP-----HQIPSTNAARTRNTKRPTMSISGYTPEEWVASRF 629
            QV RARQ +ANV+EDLLA R+ADSYWHP      QI  +NAARTRNTKRPTM+I+GYTPEEWVASR 
Sbjct:  118 QVTRARQHLANVEEDLLASRLADSYWHPCQISPDQISPSNAARTRNTKRPTMAIAGYTPEEWVASRL 184          
BLAST of SMED30028707 vs. Planmine SMEST
Match: SMESG000020448.1 (SMESG000020448.1)

HSP 1 Score: 133.65 bits (335), Expect = 1.826e-54
Identity = 75/102 (73.53%), Postives = 85/102 (83.33%), Query Frame = -1
Query:  637 MEFLLNPDEITKKXXXXXXXXXXXELTPATTAINSTSQISISLADRWRWAWAQHRQEKCPDFPPSKFLYRNNLWMGTSTQWSPTEEIYRQARQQLEDLVAQQ 942
            MEF L+ DE T KSGMSS  E SG+L  AT AINST    ISLADRWRWAW Q+RQE+CPDFPPSKFL R+N+ MGTSTQWSP+EEIY+QARQQLE+LV+QQ
Sbjct:    1 MEFSLHSDEATIKSGMSSGEEGSGKLVSATIAINST----ISLADRWRWAWVQYRQERCPDFPPSKFLDRDNMGMGTSTQWSPSEEIYQQARQQLENLVSQQ 98          

HSP 2 Score: 99.3673 bits (246), Expect = 1.826e-54
Identity = 50/67 (74.63%), Postives = 55/67 (82.09%), Query Frame = -2
Query:  444 QVARARQQIANVKEDLLAGRIADSYWHPHQI-----PSTNAARTRNTKRPTMSISGYTPEEWVASRF 629
            QV RARQ +ANV++DLLAGRIADSYWH HQI     P  NAARTRNTKRPTM+IS YTPEE VAS+F
Sbjct:  104 QVTRARQLLANVEKDLLAGRIADSYWHLHQISPDQTPPNNAARTRNTKRPTMAISCYTPEELVASQF 170          
BLAST of SMED30028707 vs. Planmine SMEST
Match: SMESG000062630.1 (SMESG000062630.1)

HSP 1 Score: 130.954 bits (328), Expect = 5.058e-54
Identity = 75/102 (73.53%), Postives = 83/102 (81.37%), Query Frame = -1
Query:  637 MEFLLNPDEITKKXXXXXXXXXXXELTPATTAINSTSQISISLADRWRWAWAQHRQEKCPDFPPSKFLYRNNLWMGTSTQWSPTEEIYRQARQQLEDLVAQQ 942
            MEF L  +E+T KS M S GE SGEL PA+TAINST    ISLADRWRWAWAQHRQE+CPDFPPSKFL R+NL  G STQW P+EEIY+QARQQLE LV+QQ
Sbjct:    1 MEFSLASNELTTKSRMQSSGEGSGELAPASTAINST----ISLADRWRWAWAQHRQERCPDFPPSKFLDRDNLGRGMSTQWIPSEEIYQQARQQLESLVSQQ 98          

HSP 2 Score: 100.523 bits (249), Expect = 5.058e-54
Identity = 49/67 (73.13%), Postives = 55/67 (82.09%), Query Frame = -2
Query:  444 QVARARQQIANVKEDLLAGRIADSYWHP-----HQIPSTNAARTRNTKRPTMSISGYTPEEWVASRF 629
            QV R RQ +ANV+EDL  GRIADSYWHP     +QIP  NAARTRNT+RPTM+I+GYTPEEWVASRF
Sbjct:  104 QVTRGRQHLANVEEDLRTGRIADSYWHPCQISLNQIPPNNAARTRNTRRPTMAIAGYTPEEWVASRF 170          
The following BLAST results are available for this feature:
BLAST of SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 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 SMED30028707 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000042929.14.928e-5571.84SMESG000042929.1[more]
SMESG000009297.11.031e-5473.53SMESG000009297.1[more]
SMESG000065282.11.298e-5470.37SMESG000065282.1[more]
SMESG000020448.11.826e-5473.53SMESG000020448.1[more]
SMESG000062630.15.058e-5473.53SMESG000062630.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028707 ID=SMED30028707|Name=SMED30028707|organism=Schmidtea mediterranea sexual|type=transcript|length=1848bp
TACCGCCTCCCCTTCACGACTAGCAGCCAGGGCGACTTCTAGCCCTCTGA
TTTGTGTCCTGAGACTCTGGTTCAACTGACGCTCCTCTGCCCAACCCAGG
TAGATTTCACCTGCTGCACTTCTTTGGTGAGTTGTATTATTTGTCCATAG
AGGGATTTGTTGGCTTGCTGGACTCGGGCCAATTCCTTTTGCAATAATTG
AGTGGGTTCCATAACTAATAAAAATAGGATTAAGTAAAGTGGTTTAAGAT
AGGGTTGTAATCGCACCATATTTGAGTTACTGCAAACAAAATTCGTATAA
CAATTAAATAATGACAAAATTTTAATCAGGCAGAAAACAAAATAAAGTCA
ATTCATAAATTTTAGTTTTAATGATCAACAATCAAATAAGCAAAATATTG
AGAGAAATACAACTAAAGTCAAATCGTCTCTGATCAGAAGGTAGAATCGG
CTCGCTACCCATTCTTCGGGTGTGTAGCCTGAGATCGACATCGTCGGTCT
CTTGGTGTTGCGGGTTCGGGCCGCATTGGTTGATGGGATCTGGTGGGGGT
GCCAGTAGGAGTCAGCAATCCGACCCGCCAGCAAATCTTCTTTTACATTC
GCTATTTGCTGGCGAGCTCGGGCCACCTGCAAAGCGTTGTTGCGCCACCA
GATCCTCCAATTGTTGCCGGGCCTGTCGATAAATCTCTTCTGTCGGGCTC
CATTGGGTGGACGTTCCCATCCATAGATTGTTCCGGTAGAGGAACTTTGA
CGGAGGGAAATCGGGACATTTTTCTTGCCGGTGTTGGGCCCAAGCCCATC
TCCAGCGATCTGCGAGGGAAATAGAGATTTGGCTTGTGGAGTTGATGGCA
GTGGTTGCGGGGGTCAATTCCCCTGACGCTTCTCCTTCCGAGGACATTCC
AGATTTCTTCGTTATTTCGTCCGGATTTAGTAAAAACTCCATGATCGTAA
AATAAACTTTCCAAGGTAGTTAATAATAATCGATTTATTCCGACAAATCT
CAGCACACTGAAAATGTTTATATTATAATTTACCAATCGATTGTCGCCTG
GACGATGATCGTGATATTTATATTAATTTCACTATCCGTTTATGGTTTGT
GTATCATGCCGGAAATGTCGAAAATCTACTTGTGTGTCGACCAATTTACC
TATAATTATTATGGAAAAATTTTAAATGATCAATGGTCAACTATTTGAAA
CTTCGTAAATGTCGATTTTGTCGGCGAATACTGATAATCTGGATTCTATC
TCGTCATGCGATTGGACAACGTGGAGGTTTCCACCAGATAGGCTGGGAGC
GGACGTAGGAAAATATTTCTATTTAATTCAGTTCGTTAGATGGCCTTTTC
CGGCGAGGTTAACGTGGAAAATATCTCGCAAAGGTTTCACGGGCATCGCA
TGGGTTTGTCAACGTAGGCCGTTCATACCATCAATAATGTTTGTTTTAAA
AATAAAAAAAATTAAAATTGTCGGGTTGTCTAATTTACTTAACCTAGCTC
AAATATTTTTAAATGTTTAAATTTTTGTCAGTTTCAGTTATGTTGATGTC
GCTTATGAGAACGTTCAAAATTCGCATTGCTATCTATAGTTTTTGGGATG
TACGTTGACTTGGGGTGAGCTTTTTCTTCACTAAAAGTTCAGGGTGAGTT
GGGTTAAATCATTACAACCATGTATTTACCGGGTTTACTAACAATTATTT
AATTAATTTATGGTTCCCCTTTAAAAATCCATACCACTTATAAGTATATG
AGAAAAGTAATCTTCTAATTACATAGCGGCGCTCCCGAAAAACACGTCGA
ATCTTAGAACCTAGTTAAATGTCTTACTTTACTAGGAATTTGAAGCGA
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protein sequence of SMED30028707-orf-1

>SMED30028707-orf-1 ID=SMED30028707-orf-1|Name=SMED30028707-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=127bp
MEFLLNPDEITKKSGMSSEGEASGELTPATTAINSTSQISISLADRWRWA
WAQHRQEKCPDFPPSKFLYRNNLWMGTSTQWSPTEEIYRQARQQLEDLVA
QQRFAGGPSSPANSECKRRFAGGSDC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000070intestinal phagocyte