SMED30016580

Overview
NameSMED30016580
Smed IDSMED30016580
Length (bp)1958
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 SMED30016580 (SMED30016580) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016580 (SMED30016580) 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 SMED30016580 (SMED30016580) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016580 (SMED30016580) 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



SMED30016580

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30016580SMESG000044545.1 dd_Smed_v4_5799_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30016580SMESG000044545.1 dd_Smed_v4_5799_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30016580SMESG000044545.1 dd_Smed_v4_5799_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30016580SMESG000044545.1 Contig4657newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30016580SMESG000044545.1 Contig4657uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30016580SMESG000016079.1 Contig4657newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30016580SMESG000016079.1 Contig4657uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30016580SMESG000044545.1 dd_Smed_v4_5799_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
SMED30016580 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001586:89181..90895 +7067
Homology
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BLAST of SMED30016580 vs. Planmine SMEST
Match: SMESG000049728.1 (SMESG000049728.1)

HSP 1 Score: 87.0409 bits (214), Expect = 1.620e-17
Identity = 100/219 (45.66%), Postives = 128/219 (58.45%), Query Frame = 2 
Query:  284 IYKIEKGVQXXXXXXXXXXXXXXFFLKHCIYNEE-KREIKGYKITDDLLKGKLTK-EMKYIGKSQKKVPT---------QKIDEQXXXXXXXXAWK*LLHQI*NNGRYNIDIKIDTFRNKNQVAMKNNFQKPSVLRKVKFQFRFQ*QTSNWNQFPK*KFRTTFKSSMLCIS*N-KSHV-----------P*IQC*A---RSFKSFR*FQKQDYY*IRFD 862
            I KIE  VQKIL  KLT+SKLTSFFLKHC+ NEE KREIK YKIT++LLKGKLTK E K+ G+S++K PT         QK+DE KSK+   +        +  NG YN D   + FR KNQ+  KN FQKP    + +FQ R +  T ++N+  +   RT+F++  L    N KS+V           P I C     R   SFR FQKQ++Y  RF+
Sbjct:  531 INKIEDPVQKILHRKLTMSKLTSFFLKHCLDNEEEKREIKRYKITENLLKGKLTKEEPKHDGESKQKGPTSNKYIKRILQKMDEDKSKTQVAAVGNNSYAAVLKNGLYNND---ENFRKKNQIDRKNEFQKP----RNQFQGR-RNFTQDFNR--RQPIRTSFQNRSLETRSNIKSYVCHEIGNFRRECPNIVCSCCGKRDHLSFRCFQKQNHYERRFE 739
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BLAST of SMED30016580 vs. Planmine SMEST
Match: SMESG000040009.1 (SMESG000040009.1)

HSP 1 Score: 60.4622 bits (145), Expect = 7.912e-11
Identity = 34/61 (55.74%), Postives = 39/61 (63.93%), Query Frame = 3 
Query:  615 RLL*KTIFKNHQ--F*GK*NFSSDFNSRHPIGTSFQNRNLEPHLNLQCFVYREISHMCHEF 791
            RL+ KT FKN +  F    NFS +FNSR PI   FQNRNLE   N+QC+ Y EI HM  EF
Sbjct:    9 RLIEKTNFKNQEINFKDSLNFSQNFNSRQPIRIFFQNRNLETRSNIQCYAYHEIGHMRREF 69
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BLAST of SMED30016580 vs. Planmine SMEST
Match: SMESG000037066.1 (SMESG000037066.1)

HSP 1 Score: 60.8474 bits (146), Expect = 9.991e-11
Identity = 28/48 (58.33%), Postives = 35/48 (72.92%), Query Frame = 3 
Query:  645 HQF*GK*NFSSDFNSRHPIGTSFQNRNLEPHLNLQCFVYREISHMCHE 788
            +QF G+ NF+ DFN+R PI TSFQNR+ E H N+QC+   EI HMC E
Sbjct:   51 NQFQGRRNFTQDFNTRQPIRTSFQNRSSETHSNIQCYACHEIGHMCRE 98
[Close]
BLAST of SMED30016580 vs. Planmine SMEST
Match: SMESG000044545.1 (SMESG000044545.1)

HSP 1 Score: 61.6178 bits (148), Expect = 3.073e-10
Identity = 30/30 (100.00%), Postives = 30/30 (100.00%), Query Frame = 3 
Query: 1608 ELNIVLEEDAGSDTDIYEKKKEKFKISQTQ 1697
            ELNIVLEEDAGSDTDIYEKKKEKFKISQTQ
Sbjct:  214 ELNIVLEEDAGSDTDIYEKKKEKFKISQTQ 243
[Close]
BLAST of SMED30016580 vs. Planmine SMEST
Match: SMESG000044545.1 (SMESG000044545.1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.852e-9
Identity = 31/46 (67.39%), Postives = 36/46 (78.26%), Query Frame = 3 
Query: 1608 ELNIVLEEDAGSDTDIYEKKKEKFKISQTQEPIKIISQSRDLKHFR 1745
            ELNIVLEEDAGSDTDIYEKKKEKFKISQ    +  +S++    +FR
Sbjct:  214 ELNIVLEEDAGSDTDIYEKKKEKFKISQVY--LNAVSRTNPQHYFR 257
The following BLAST results are available for this feature:
BLAST of SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 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 SMED30016580 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000049728.11.620e-1745.66SMESG000049728.1[more]
SMESG000040009.17.912e-1155.74SMESG000040009.1[more]
SMESG000037066.19.991e-1158.33SMESG000037066.1[more]
SMESG000044545.13.073e-10100.00SMESG000044545.1[more]
SMESG000044545.11.852e-967.39SMESG000044545.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016580 ID=SMED30016580|Name=SMED30016580|organism=Schmidtea mediterranea sexual|type=transcript|length=1958bp
TCAACAAAGAAAAGTGATTGTTTGAGCATTTTTGGCTGAAAATTGTTGCA
ACAAATATGATAAAATTCCTGACCAAAAGGTTATTTGAAAAGACGTTATG
TGCTGTAGACACACAAGAAGCATGTATGTAATTTATTGACTTTTTCATAA
ATAAACCTCACTGACATTGTTTTTTTGATCATATAATATGACCTCCACTC
TTTCAACTCAAGAAGTATTGCGAATATTTTACCGAGAAATAATTCAATTG
GACATCAAAAAAAAGATCATGATGCAGAAACTTATCTACAAGATCGAAAA
AGGTGTACAGAAGATTTTGAAGCACAAATTAACACTTTCAAAGCTGACAT
CGTTCTTTCTAAAACATTGCATTTACAACGAAGAAAAGCGTGAAATAAAA
GGTTATAAAATTACTGATGATTTACTTAAAGGAAAGTTAACGAAAGAAAT
GAAATATATTGGAAAATCACAAAAGAAAGTCCCAACGCAGAAAATAGATG
AACAGAAATCAAAGTCATAAAGTGTCAGCGCTTGGAAATAACTCTTGCAT
CAGATTTAAAATAATGGTCGATACAATATTGATATAAAAATCGATACTTT
CAGAAATAAAAACCAGGTTGCTATGAAAAACAATTTTCAAAAACCATCAG
TTTTAAGGAAAGTGAAATTTCAGTTCAGATTTCAATAGCAGACATCCAAT
TGGAACCAGTTTCCAAAATAGAAATTTAGAACCACATTTAAATCTTCAAT
GCTTTGTATATCGTGAAATAAGTCACATGTGCCATGAATTCAATGTTAAG
CAAGGTCATTTAAAAGTTTTAGGTGATTTCAGAAGCAGGATTACTATTAA
ATAAGATTTGATTGTATCATTGTTTGATACTGGGAGTTATTGAATTACGG
TTTTCTTGAATAAAAATACAGTATAAATTATTACATTTTTATTACATTTA
TAGAAATCTAGATGGGTAGTTTTGTTGTTTATTTAGAGAACTTAAATTAT
TTTAACATATAAAAGACAATATTATATCTTTGGTTTTAATAATAATGGTT
ATAAAGTTAGTAATTTTTGTGCGGCCTTTCACAAGTCTAAAATTGTTAAT
GCGACCCAAGGCATGGGTTGAGTTTTATAATCCTGATGTGAGCTTATATC
ACTGCTCTTCCAAAGAACAACATCAGGGTGAGTTTGTATGTATCTTTATT
ATAAGGTTATTGAAAATTGGCAATACACTTAAATCCCTAACCATTCTGTC
CTTCTGAAATCCAATTTCAAAATTGTGAAAAAATTTCTATTTTTCTCTTA
ATTTTGACTTAATTTAGAGTGAAAATTATCATTTTATTTTGACAGTGTAA
AATATTAGTGAAAATCTGACGAAATTTCTCCTAATATTTAGCCGTTTATG
CATGGCATACAAGAACGCTAAATGTATAAAAATCAGTTTTTATGTGTTTT
TATTACGGAACAGTCCTGGTAATGATGTTTTTGTCCAAACTGGACACCAA
ATTCAAAAGCCTTTTTAGTATTTATTTTTTCAATGAACAAAAACCCACTA
AATATATTCTATTAATTTTTACATATATCTCGCTATTTCAGTTTTTATGT
GATTTTAGAGCTCAATATTGTTTTGGAGGAAGATGCTGGATCCGACACAG
ATATTTATGAAAAGAAGAAAGAGAAATTCAAAATTTCTCAGACTCAAGAA
CCAATCAAAATCATCAGCCAATCACGAGATCTAAAACATTTTCGAATTGA
CCTTTCAAACTTATCGAATCTCAAGTATGATGCGCCTAAACTCGATTGCT
TTCAAATGCTTTATTTTCACTCGTGATTGCACATATTGAATATTGCGCGT
TTCAGTTGATTATTTATTCTGTTAAAGCAAGATGAAAACATTTTCTCGGA
GTAAATATTGATTTTTCGGTCTATTTTTGTTGAAATGTAGAGATGTAAGC
AAAATATA
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protein sequence of SMED30016580-orf-1

>SMED30016580-orf-1 ID=SMED30016580-orf-1|Name=SMED30016580-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
MTSTLSTQEVLRIFYREIIQLDIKKKIMMQKLIYKIEKGVQKILKHKLTL
SKLTSFFLKHCIYNEEKREIKGYKITDDLLKGKLTKEMKYIGKSQKKVPT
QKIDEQKSKS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000101muscle cell