SMED30031120

Overview
NameSMED30031120
Smed IDSMED30031120
Length (bp)2223
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 SMED30031120 (SMED30031120) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031120 (SMED30031120) 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 SMED30031120 (SMED30031120) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031120 (SMED30031120) 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



SMED30031120

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
X1 cellSMED30031120SMESG000036622.1 SmedASXL_014730SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30031120SMESG000036622.1 dd_Smed_v4_9680_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30031120SMESG000036622.1 dd_Smed_v4_9680_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30031120SMESG000036622.1 dd_Smed_v4_9680_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30031120SMESG000036622.1 dd_Smed_v4_9680_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031120 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001836:18806..32648 -10820
Homology
[Close]
BLAST of SMED30031120 vs. Planmine SMEST
Match: SMESG000036622.1 (SMESG000036622.1)

HSP 1 Score: 1214.52 bits (3141), Expect = 0.000e+0
Identity = 698/705 (99.01%), Postives = 699/705 (99.15%), Query Frame = 3 
Query:   75 MELEKIKLNLKGVIGSSKDGILVNNLESEYKKITNSSLNYKNYNQSLIGFLTSMNDMVRLQYTNYGCYVHLSNNENAPQCLKKLCNLIQXXXXXXXXXXXYNIPNNIMSKANGYNNLKISVPNDLWSTYHETXXXXXXXXXXXXXXXXXXXXXXXXYQSRVNNSYSQNDSYKYPNNANQSYNKIXXXXXXXXXXXXXXXKNYPNVNNTPAYSSMSSYVQASNKLPNEKPFVTDNSCGQSNGFKSPIVDSSASKTINDRSLNSYGSQPKQNSYLNMNNTPAYSPMSSCTQASNKLPNDKPRVTDSKISTNESFQXXXXXXXXXXXXXXXXXXXXXQPFSNIGVSHQNETISAINMNKEESFIIDWPINLDISIDILHKPVRILGIQSGYALLTVGNTVSKSVYIPANSFFSMFPGDIFLWQPPIPDSNRSKSMIDICNAVPIIAIEQINDTMKVRVMGLKVLLIVHIHDVYXXXXXXXXXXXXLSEFEVRKLTFTRLAMIPKFVNYYNTDLLSDLYFSPDSFSDNEFIFERCEKRGDFLNIMILIRYLNSDLRQISSSDQNIFVRNIVIALDNAKSALCNQVRAMLGGKSSECDMLLPIEHNRTPLKDRMLIGCERILSSHNETNENDLNLERMIYNDQNTGFYYLDSNSQTTAVFSTNSPIRGIYRINDEFVTSRLSNVTKFRFQISLLIRIPSVFKFRNISNKI 2189
            MELEKIKLNLKGVIGSSKDGILVNNLESEYKKITNSSLNYKNYNQSLIGFLTSMNDMVRLQYTNYGCYVHLSNNENAPQCLKKLCNLIQTTKSKKTTKKKYNIPNNIMSKANGYNNLKISVPNDLWSTYHETNGNGFDVRNNTNNNNSVGLNTINGYQSRVNNSYSQNDSYKYPNNAN SYNKILNEQSLNSSNLQ RQKNYPNVNNTPAYSSMSSYVQASNKLPNEKPFVTDNSCGQSNGFKSPIVDSSASKTINDRSLNSYGSQPKQNSYLNMNNTPAYSPMSSC QASNKLPNDKPRVTDSKISTNESFQSNSKPYSISSSSTNSLDIISNQPFSNIGVSHQNETISAINMNKEESFIIDWPINLDISIDILHKPVRILGIQSGYALLTVGNTVSKSVYIPANSFFSMFPGDIFLWQPPIPDSNRSKSMIDICNAVPIIAIEQINDTMKVRVMGLKVLLIVHIHDVYKFPNNIFNFKKFLSEFEVRKLTFTRLAMIPKFVNYYNTDLLSDLYFSPDSFSDNEFIFERCEKRGDFLNIMILIRYLNSDLRQISSSDQNIFVRNIVIALDNAKSAL NQVRAMLGGKSSECDMLLPI+HNRTPLKDRMLIGCERILSSHNETNENDLNLERMIYNDQNTGFYY DSNSQTTAVFSTNSPIRGIYRINDEFVTSRLSNVTKFRFQISLLIRIPSV KFRNISNKI
Sbjct:    1 MELEKIKLNLKGVIGSSKDGILVNNLESEYKKITNSSLNYKNYNQSLIGFLTSMNDMVRLQYTNYGCYVHLSNNENAPQCLKKLCNLIQTTKSKKTTKKKYNIPNNIMSKANGYNNLKISVPNDLWSTYHETNGNGFDVRNNTNNNNSVGLNTINGYQSRVNNSYSQNDSYKYPNNANPSYNKILNEQSLNSSNLQLRQKNYPNVNNTPAYSSMSSYVQASNKLPNEKPFVTDNSCGQSNGFKSPIVDSSASKTINDRSLNSYGSQPKQNSYLNMNNTPAYSPMSSCNQASNKLPNDKPRVTDSKISTNESFQSNSKPYSISSSSTNSLDIISNQPFSNIGVSHQNETISAINMNKEESFIIDWPINLDISIDILHKPVRILGIQSGYALLTVGNTVSKSVYIPANSFFSMFPGDIFLWQPPIPDSNRSKSMIDICNAVPIIAIEQINDTMKVRVMGLKVLLIVHIHDVYKFPNNIFNFKKFLSEFEVRKLTFTRLAMIPKFVNYYNTDLLSDLYFSPDSFSDNEFIFERCEKRGDFLNIMILIRYLNSDLRQISSSDQNIFVRNIVIALDNAKSALYNQVRAMLGGKSSECDMLLPIDHNRTPLKDRMLIGCERILSSHNETNENDLNLERMIYNDQNTGFYYFDSNSQTTAVFSTNSPIRGIYRINDEFVTSRLSNVTKFRFQISLLIRIPSVLKFRNISNKI 705
The following BLAST results are available for this feature:
BLAST of SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 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 SMED30031120 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000036622.10.000e+099.01SMESG000036622.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031120 ID=SMED30031120|Name=SMED30031120|organism=Schmidtea mediterranea sexual|type=transcript|length=2223bp
GTTTTTTTTGATTTTAAGCATTCATTGGTAAAATATTTATTGTAATAAGA
ACTATTCTTCAAAAAATTAAGAGTATGGAATTAGAAAAAATTAAATTAAA
TCTTAAAGGAGTTATCGGATCATCTAAAGATGGGATTCTTGTTAACAATT
TAGAAAGTGAATATAAAAAAATAACAAACTCCTCTTTAAATTACAAAAAT
TATAATCAAAGTCTTATTGGATTTCTTACCTCGATGAATGATATGGTTAG
ACTTCAATATACTAACTATGGTTGTTATGTCCATCTTTCTAATAATGAGA
ATGCTCCACAGTGCTTAAAAAAGCTTTGTAATCTCATACAGACTACAAAA
TCAAAAAAAACTACGAAAAAAAAATACAATATTCCAAATAATATTATGTC
AAAGGCCAATGGATATAATAATCTGAAAATTTCGGTCCCAAATGACTTAT
GGTCAACTTATCATGAAACCAATGGAAATGGATTTGACGTGCGCAACAAT
ACAAACAATAATAATTCTGTGGGACTCAACACTATCAATGGGTATCAAAG
TCGTGTCAATAATTCCTATAGCCAAAATGACAGTTACAAATATCCTAATA
ATGCCAATCAATCTTATAATAAAATACTTAATGAGCAATCATTGAATAGT
TCTAATTTGCAATCAAGACAAAAAAATTATCCAAATGTGAATAACACTCC
TGCATACTCTTCAATGTCTAGCTATGTTCAAGCATCAAATAAATTACCTA
ATGAGAAACCATTTGTAACTGATAATTCTTGTGGCCAGAGTAACGGTTTC
AAAAGTCCTATTGTCGATTCATCTGCTAGCAAAACAATAAATGATCGATC
ATTGAATAGCTACGGTTCACAACCAAAACAGAACTCTTATCTAAATATGA
ATAACACTCCTGCATACTCACCGATGTCTAGCTGCACTCAGGCGTCTAAC
AAATTACCTAATGACAAACCGCGTGTAACTGATAGTAAAATCAGCACAAA
TGAATCATTCCAATCCAATTCAAAACCTTACTCGATTTCCTCTTCATCAA
CCAATAGCTTAGATATAATATCAAATCAGCCATTTAGCAATATAGGCGTT
TCTCATCAAAATGAAACGATAAGCGCGATCAATATGAACAAGGAAGAATC
ATTCATCATTGATTGGCCAATAAATTTGGATATCAGTATTGATATTTTGC
ATAAACCCGTCAGGATTCTTGGAATTCAGTCGGGATATGCACTTTTAACG
GTCGGCAATACTGTCTCTAAAAGTGTATATATTCCTGCAAATTCATTTTT
TTCGATGTTTCCAGGAGATATTTTCCTTTGGCAACCCCCAATTCCTGATT
CTAATCGCTCGAAATCTATGATTGACATTTGTAACGCTGTTCCTATCATT
GCAATCGAACAAATTAACGATACAATGAAGGTTCGAGTCATGGGGCTCAA
AGTCTTGTTAATAGTTCACATTCATGATGTTTACAAGTTCCCCAATAATA
TTTTCAATTTCAAAAAGTTTCTATCAGAATTTGAAGTTAGAAAATTGACA
TTTACCCGACTGGCAATGATTCCAAAATTTGTCAATTATTATAATACGGA
TCTTTTGTCAGACCTCTATTTTTCTCCCGACTCATTTAGTGACAACGAGT
TCATCTTTGAACGATGTGAAAAACGCGGGGATTTTTTAAATATAATGATA
CTAATCCGTTATTTGAATTCGGATTTACGGCAGATAAGTTCTAGTGATCA
AAATATATTTGTGAGAAATATTGTTATTGCGTTAGACAACGCTAAGTCAG
CTTTATGCAATCAAGTACGAGCTATGTTGGGAGGAAAGTCATCAGAATGT
GATATGCTGTTACCAATAGAGCACAATCGAACTCCGTTGAAAGATCGGAT
GTTGATTGGATGTGAAAGGATATTATCATCGCACAATGAGACAAATGAAA
ATGATCTAAACTTAGAAAGAATGATTTATAACGATCAAAATACTGGTTTT
TATTATTTGGATAGTAATTCGCAAACAACGGCGGTCTTTTCCACAAATTC
CCCGATTAGAGGTATCTATCGAATTAATGATGAGTTTGTAACTTCTAGAT
TGTCAAATGTTACCAAATTTCGATTTCAAATCTCACTTTTGATTCGTATT
CCGTCGGTTTTTAAATTCAGAAATATCTCGAATAAAATTTGATCGATTTT
ATAATAATAAAATACATAAATTG
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protein sequence of SMED30031120-orf-1

>SMED30031120-orf-1 ID=SMED30031120-orf-1|Name=SMED30031120-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=706bp
MELEKIKLNLKGVIGSSKDGILVNNLESEYKKITNSSLNYKNYNQSLIGF
LTSMNDMVRLQYTNYGCYVHLSNNENAPQCLKKLCNLIQTTKSKKTTKKK
YNIPNNIMSKANGYNNLKISVPNDLWSTYHETNGNGFDVRNNTNNNNSVG
LNTINGYQSRVNNSYSQNDSYKYPNNANQSYNKILNEQSLNSSNLQSRQK
NYPNVNNTPAYSSMSSYVQASNKLPNEKPFVTDNSCGQSNGFKSPIVDSS
ASKTINDRSLNSYGSQPKQNSYLNMNNTPAYSPMSSCTQASNKLPNDKPR
VTDSKISTNESFQSNSKPYSISSSSTNSLDIISNQPFSNIGVSHQNETIS
AINMNKEESFIIDWPINLDISIDILHKPVRILGIQSGYALLTVGNTVSKS
VYIPANSFFSMFPGDIFLWQPPIPDSNRSKSMIDICNAVPIIAIEQINDT
MKVRVMGLKVLLIVHIHDVYKFPNNIFNFKKFLSEFEVRKLTFTRLAMIP
KFVNYYNTDLLSDLYFSPDSFSDNEFIFERCEKRGDFLNIMILIRYLNSD
LRQISSSDQNIFVRNIVIALDNAKSALCNQVRAMLGGKSSECDMLLPIEH
NRTPLKDRMLIGCERILSSHNETNENDLNLERMIYNDQNTGFYYLDSNSQ
TTAVFSTNSPIRGIYRINDEFVTSRLSNVTKFRFQISLLIRIPSVFKFRN
ISNKI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR041966LOTUS-like
IPR025605OST-HTH/LOTUS_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR041966LOTUS-like domainGENE3DG3DSA:1.10.10.1880coord: 1..77
e-value: 2.5E-11
score: 45.5
IPR025605OST-HTH/LOTUS domainPFAMPF12872OST-HTHcoord: 2..65
e-value: 7.6E-5
score: 22.5
IPR025605OST-HTH/LOTUS domainPROSITEPS51644HTH_OSTcoord: 2..73
score: 12.676