SMED30009384

Overview
NameSMED30009384
Smed IDSMED30009384
Length (bp)2875
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 SMED30009384 (SMED30009384) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009384 (SMED30009384) 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 SMED30009384 (SMED30009384) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009384 (SMED30009384) 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




SMED30009384

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
epidermisSMED30009384h1SMcG0006793 dd_Smed_v4_11603_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30009384h1SMcG0006793 dd_Smed_v4_11603_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
Homology
BLAST of SMED30009384 vs. Planmine SMEST
Match: SMESG000054833.1 (SMESG000054833.1)

HSP 1 Score: 922.924 bits (2384), Expect = 0.000e+0
Identity = 495/507 (97.63%), Postives = 499/507 (98.42%), Query Frame = 2
Query:  131 MNAENQLSDDTEVLIQPENQNQNFYEDLSDXXXXXXXXXXXXXHFLASCAIFCFEFGYKTHRLKFTDSLILLKNLSFILIGTIIIVGYRPNQRNPATQISNLRNPTILYLIIVPMTAVCGLTSLLESYLYLGKISCRGYMXXXXXXXXXXXXXXXXXXXNDIDRIFIRQAAIIGNIFKKSVLSLITVSCFGIYLAEMSKRLSLNKNQIFNFQNFSVEYFKDLENEYLQIYRILYVYKKYVTFTSVGYAICLIFYVIPLLKLIRSKPSINENRESQVLTNRNSSNKEISVLSIIAIMILISVTILAILFEDFFMIPDETLSTFGKTISYLKTSCELLSNICVVALSLIVIQGLSKSKTLPTKQPFSITNQCFAWGGLFGSFLKLISNILLFITTEHSILVYFNSLFKLISVTFQAFLIDMLATRSYQRRRKYSWTDGIQPFVLLSGANLYFIFCDVIDVILINSRIIESKNPVATVAMQILLQAFSFDLIFLQRFHALIYFMNLFKKN 1651
            MNAENQLSDDTEVLIQPENQNQNFYEDLSDSIVILIGVILISIHFLASCAIFCFEFGYKTHRLKFTDSLILLKNLSFILIGTIIIVGYRPNQRNPATQISNLRNPTILYLIIVPMTAVCGLTSLLES LYLGKISCRGYMFSFLE FVVSFVILVLVVLNDIDRIFIRQAAIIGNIFKKSVL LITVSCFGIYLAEMSKRLSLNKNQIFNFQNFSVEYFKDLENEYLQ+YRILYVYKKYVTFTSVGYAICLIFYVIPLLKLIRSKPSINENRESQVLTNRNSSNKEISVLSIIAIMILISVTILAILFEDFFMIPD+TLSTFG+TI YLKT CELLSNICVVALSLIVIQGLSKSKT PTKQPFSITNQCFAWGGLFGSFLKLISNILLFITTEHSILVYFNSLFK ISVTFQAFLIDMLATRSYQRRRKYSWTDGIQPFVLLSGANLYFIFCDVIDVILINSRIIESKNP ATVAMQILLQAFSFDLIFLQRFHALIYFM+LFKKN
Sbjct:    1 MNAENQLSDDTEVLIQPENQNQNFYEDLSDSIVILIGVILISIHFLASCAIFCFEFGYKTHRLKFTDSLILLKNLSFILIGTIIIVGYRPNQRNPATQISNLRNPTILYLIIVPMTAVCGLTSLLESSLYLGKISCRGYMFSFLEGFVVSFVILVLVVLNDIDRIFIRQAAIIGNIFKKSVLLLITVSCFGIYLAEMSKRLSLNKNQIFNFQNFSVEYFKDLENEYLQMYRILYVYKKYVTFTSVGYAICLIFYVIPLLKLIRSKPSINENRESQVLTNRNSSNKEISVLSIIAIMILISVTILAILFEDFFMIPDKTLSTFGETIVYLKTFCELLSNICVVALSLIVIQGLSKSKTFPTKQPFSITNQCFAWGGLFGSFLKLISNILLFITTEHSILVYFNSLFKFISVTFQAFLIDMLATRSYQRRRKYSWTDGIQPFVLLSGANLYFIFCDVIDVILINSRIIESKNPAATVAMQILLQAFSFDLIFLQRFHALIYFMHLFKKN 507          
The following BLAST results are available for this feature:
BLAST of SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 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 SMED30009384 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000054833.10.000e+097.63SMESG000054833.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009384 ID=SMED30009384|Name=SMED30009384|organism=Schmidtea mediterranea sexual|type=transcript|length=2875bp
CTAAAATGAAGAGTGATGCTGAGTTGCTTTACACCGATGCATTTCACAAT
ATTATTGATTTGATGAAGTTTTACATCTGTGTCACACCATTGTTGTCTAA
ACAACAGAATAATCAATCGCAACTTACAAAATGAATGCAGAAAATCAGTT
ATCTGACGACACAGAAGTTCTCATCCAACCAGAAAATCAAAATCAAAACT
TCTACGAGGACCTTTCTGACTCAATTGTGATACTAATTGGGGTTATTTTG
ATATCAATCCATTTCTTAGCATCATGTGCAATTTTTTGTTTTGAGTTTGG
CTATAAAACTCATAGATTGAAATTCACTGATTCACTGATACTTCTGAAAA
ATCTTTCATTCATATTAATCGGAACAATCATTATTGTTGGGTATCGGCCA
AACCAACGAAACCCAGCTACCCAGATCTCGAACTTGCGAAACCCAACTAT
TTTATATTTAATAATAGTCCCAATGACTGCAGTCTGCGGTCTAACGAGTT
TGCTGGAATCGTATTTATATTTAGGTAAAATTAGTTGTCGTGGGTATATG
TTTTCGTTTTTAGAGGTTTTTGTGGTTAGTTTCGTTATTTTGGTCCTAGT
GGTGCTTAATGACATTGATAGAATATTTATCAGACAAGCAGCAATCATTG
GGAATATATTCAAAAAATCTGTTTTGTCGTTGATTACCGTCTCTTGTTTT
GGAATATATCTGGCTGAAATGAGTAAAAGACTAAGCCTCAACAAAAATCA
AATATTTAATTTCCAAAATTTCTCCGTTGAATATTTCAAAGACCTAGAGA
ATGAATATTTACAAATTTATCGCATATTATACGTATATAAAAAGTATGTC
ACTTTTACATCAGTTGGATATGCGATCTGTTTAATATTTTATGTGATTCC
ACTATTGAAACTGATTCGTTCAAAACCTTCGATCAATGAAAATCGAGAAT
CGCAAGTATTAACCAATCGAAACTCGTCTAATAAAGAGATTTCCGTTTTG
TCAATTATTGCTATAATGATTTTAATTAGCGTGACGATTTTGGCTATTCT
GTTTGAAGATTTTTTTATGATTCCTGATGAAACATTGAGTACTTTTGGAA
AGACAATTTCTTATTTGAAGACTTCTTGTGAATTATTAAGCAACATATGC
GTTGTTGCACTGTCATTAATTGTAATACAAGGACTCTCTAAATCTAAAAC
ATTGCCTACTAAGCAACCTTTCTCGATCACTAATCAGTGCTTTGCATGGG
GTGGATTATTTGGGAGTTTCTTGAAACTTATTTCAAATATTCTTCTGTTT
ATTACAACCGAACATTCGATTTTAGTGTATTTCAATTCTTTGTTCAAATT
GATTTCTGTTACTTTTCAAGCTTTTCTCATTGATATGTTGGCAACTAGAT
CTTACCAAAGGCGTCGAAAGTATTCATGGACCGATGGAATTCAACCATTC
GTTCTGTTATCAGGTGCAAATCTTTATTTCATTTTCTGCGACGTGATTGA
TGTAATCCTAATTAATTCACGAATAATTGAATCAAAAAATCCAGTTGCAA
CAGTTGCCATGCAAATTCTGTTACAAGCCTTTAGTTTTGATTTGATTTTC
TTGCAACGTTTTCACGCTTTGATATATTTTATGAACTTATTCAAAAAAAA
CTAGTATTGTAACGATTCGAATAGTTTAGATCCAAATTCTGGATCTGAAA
TTGGAAATAATAGACAATTTTATTTTCATTTGTTAATCATTCTACAGAAA
TAATACATTTCTATTTGTTGAATTCCAGTGCATTCTTCTTCGCCTAGACC
AGGGGTTCTTAACCTTTTTTACTTCATACCTCACCTAATATTTAATTTTA
TGTTCTCACCTCCAGCATAATTAATTTATTTTAAGAAAAGATAAGAAACA
TAATTAGTGGTGTACCAACATTACATATATTATTTTATTTTTACCATTTT
AATATATATTTATAAAAAAAATCATATTTAATTCATACTGATATAAAAAA
TTATATTTTATATTAAATTTCATGTTGACAAAATTTATTTATGTGAAAAA
TTTATGTGAAAACAAAATCTCATACCTCCCCCAACACATTAGTATACCTC
CCCAAGGGAGGTATACCTCACCGGTTAAGAAACCCTGCTCTAGGAATATA
TATATTTAAGGTTTTATAGCTTACCCAGTATATCGTTTTATATCTATTAG
TTTGATTTTGAAATTAAGTTGTTTTAATTGCTCAACTTAAAGTATTGTAG
TTTAATTACCCTAAAATCTCACATATAAACCACAGCTTATATAAAAAAAT
GATTTAAAAGAAAATAGTGAGTTTCGGCTTATAATCAACGTGGCAGATAT
GAGAGAGTTTGGGGTATCCAAAAGTCAAACATCTCGTATAAAAACCGCAC
CACATGTTTTAAGCTGAAAAAACCCACTGTTTACATTATGAGACGTCCAT
TAATTATGTCATCAATTTTAAGGCAATTTTAAACCCCTTCCCTTGTCAAC
AATTATCAAACTTCCAGCGAAGCCCTTAAAATAATTATGTCAAACAAATT
TTACCCTTCCCCCTTACAAACTATTTACATTTTGTAGGATATTTTATAGA
ATATTTCGTTTATACAAGCCAATCAACTCGTTTTTGATGTTGTTTATCTG
ACCCTGCAACTCGCCTTGAGTTTTTGTTTTGTACATGACAGATTTTGCTT
TATATTACATATTGCAAACGAATTTATGTATAAATTTTAATAATAATAAT
ATTTACTTACTTACCTATCCTACGCCCTCTGGAGAATACCGTCCTTTAGA
AATAAAAATCTGGCGTGTAAATATATTATAAATATTAAAAATTAAATCAT
ATAATTGAATAATTTTAAAAAAGTC
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protein sequence of SMED30009384-orf-1

>SMED30009384-orf-1 ID=SMED30009384-orf-1|Name=SMED30009384-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=508bp
MNAENQLSDDTEVLIQPENQNQNFYEDLSDSIVILIGVILISIHFLASCA
IFCFEFGYKTHRLKFTDSLILLKNLSFILIGTIIIVGYRPNQRNPATQIS
NLRNPTILYLIIVPMTAVCGLTSLLESYLYLGKISCRGYMFSFLEVFVVS
FVILVLVVLNDIDRIFIRQAAIIGNIFKKSVLSLITVSCFGIYLAEMSKR
LSLNKNQIFNFQNFSVEYFKDLENEYLQIYRILYVYKKYVTFTSVGYAIC
LIFYVIPLLKLIRSKPSINENRESQVLTNRNSSNKEISVLSIIAIMILIS
VTILAILFEDFFMIPDETLSTFGKTISYLKTSCELLSNICVVALSLIVIQ
GLSKSKTLPTKQPFSITNQCFAWGGLFGSFLKLISNILLFITTEHSILVY
FNSLFKLISVTFQAFLIDMLATRSYQRRRKYSWTDGIQPFVLLSGANLYF
IFCDVIDVILINSRIIESKNPVATVAMQILLQAFSFDLIFLQRFHALIYF
MNLFKKN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 240..262
NoneNo IPR availableTMHMMTMhelixcoord: 397..419
NoneNo IPR availableTMHMMTMhelixcoord: 172..194
NoneNo IPR availableTMHMMTMhelixcoord: 327..349
NoneNo IPR availableTMHMMTMhelixcoord: 288..307
NoneNo IPR availableTMHMMTMhelixcoord: 108..130
NoneNo IPR availableTMHMMTMhelixcoord: 440..462
NoneNo IPR availableTMHMMTMhelixcoord: 69..88
NoneNo IPR availableTMHMMTMhelixcoord: 32..54
NoneNo IPR availableTMHMMTMhelixcoord: 370..392
NoneNo IPR availableTMHMMTMhelixcoord: 140..159
NoneNo IPR availableTMHMMTMhelixcoord: 472..491