SMED30015116

Overview
NameSMED30015116
Smed IDSMED30015116
Length (bp)1186
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 SMED30015116 (SMED30015116) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015116 (SMED30015116) 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 SMED30015116 (SMED30015116) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015116 (SMED30015116) 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



SMED30015116

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30015116h1SMcG0014828 dd_Smed_v4_5552_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30015116h1SMcG0014828 dd_Smed_v4_5552_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30015116h1SMcG0014828 dd_Smed_v4_5552_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
SMED30015116 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000107:16066..17299 +5903
Homology
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BLAST of SMED30015116 vs. Planmine SMEST
Match: SMESG000012426.1 (SMESG000012426.1)

HSP 1 Score: 374.785 bits (961), Expect = 6.896e-155
Identity = 193/193 (100.00%), Postives = 193/193 (100.00%), Query Frame = 1 
Query:  454 NKVEVFTNFQSYSLXXXXXXXXXXXTEKYDILTKPKDLFIQSTSKRLGSGWFDNSNEIACFRWEIKNLLNLRNRNQEIASGYFFSHCRQYEMWLYFYPKGSEYNDDFQISFRLWIQSSHKYDSKWPFLGQVTLAIWNSKKPTLQESITVQLNGNISLLRPFYRSDPINFSFPKLQISNDFDSLTSYCSVSCCE 1032
            NKVEVFTNFQSYSLDNDKNKKQNDKTEKYDILTKPKDLFIQSTSKRLGSGWFDNSNEIACFRWEIKNLLNLRNRNQEIASGYFFSHCRQYEMWLYFYPKGSEYNDDFQISFRLWIQSSHKYDSKWPFLGQVTLAIWNSKKPTLQESITVQLNGNISLLRPFYRSDPINFSFPKLQISNDFDSLTSYCSVSCCE
Sbjct:   93 NKVEVFTNFQSYSLDNDKNKKQNDKTEKYDILTKPKDLFIQSTSKRLGSGWFDNSNEIACFRWEIKNLLNLRNRNQEIASGYFFSHCRQYEMWLYFYPKGSEYNDDFQISFRLWIQSSHKYDSKWPFLGQVTLAIWNSKKPTLQESITVQLNGNISLLRPFYRSDPINFSFPKLQISNDFDSLTSYCSVSCCE 285

HSP 2 Score: 192.586 bits (488), Expect = 6.896e-155
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = 3 
Query:  138 MVNFKDIQKHFKISKIDKSFCAICNGHVGDTRGELCQCLYCKNCLTKFMNLNKNLFHLKDCKFHRPFNSIFEKSKNWFIETEGRQNKNIKSE 413
            MVNFKDIQKHFKISKIDKSFCAICNGHVGDTRGELCQCLYCKNCLTKFMNLNKNLFHLKDCKFHRPFNSIFEKSKNWFIETEGRQNKNIKSE
Sbjct:    1 MVNFKDIQKHFKISKIDKSFCAICNGHVGDTRGELCQCLYCKNCLTKFMNLNKNLFHLKDCKFHRPFNSIFEKSKNWFIETEGRQNKNIKSE 92
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BLAST of SMED30015116 vs. Planmine SMEST
Match: SMESG000012426.1 (SMESG000012426.1)

HSP 1 Score: 293.123 bits (749), Expect = 1.619e-130
Identity = 159/176 (90.34%), Postives = 161/176 (91.48%), Query Frame = 1 
Query:  454 NKVEVFTNFQSYSLXXXXXXXXXXXTEKYDILTKPKDLFIQSTSKRLGSGWFDNSNEIACFRWEIKNLLNLRNRNQEIASGYFFSHCRQYEMWLYFYPKGSEYNDDFQISFRLWIQSSHKYDSKWPFLGQVTLAIWNSKKPTLQESITVQLNGNISLLRPFYRSDPINFSFPKLQI 981
            NKVEVFTNFQSYSLDNDKNKKQNDKTEKYDILTKPKDLFIQSTSKRLGSGWFDNSNEIACFRWEIKNLLNLRNRNQEIASGYFFSHCRQYEMWLYFYPKGSEYNDDFQISFRLWIQSSHKYDSKWPFLGQVTLAIWNSKKPTLQESITVQL  N+SL          NF FP + I
Sbjct:   93 NKVEVFTNFQSYSLDNDKNKKQNDKTEKYDILTKPKDLFIQSTSKRLGSGWFDNSNEIACFRWEIKNLLNLRNRNQEIASGYFFSHCRQYEMWLYFYPKGSEYNDDFQISFRLWIQSSHKYDSKWPFLGQVTLAIWNSKKPTLQESITVQL--NVSL----------NFRFPTILI 256

HSP 2 Score: 192.971 bits (489), Expect = 1.619e-130
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = 3 
Query:  138 MVNFKDIQKHFKISKIDKSFCAICNGHVGDTRGELCQCLYCKNCLTKFMNLNKNLFHLKDCKFHRPFNSIFEKSKNWFIETEGRQNKNIKSE 413
            MVNFKDIQKHFKISKIDKSFCAICNGHVGDTRGELCQCLYCKNCLTKFMNLNKNLFHLKDCKFHRPFNSIFEKSKNWFIETEGRQNKNIKSE
Sbjct:    1 MVNFKDIQKHFKISKIDKSFCAICNGHVGDTRGELCQCLYCKNCLTKFMNLNKNLFHLKDCKFHRPFNSIFEKSKNWFIETEGRQNKNIKSE 92
[Close]
BLAST of SMED30015116 vs. Planmine SMEST
Match: SMESG000012339.1 (SMESG000012339.1)

HSP 1 Score: 64.3142 bits (155), Expect = 4.894e-11
Identity = 49/148 (33.11%), Postives = 78/148 (52.70%), Query Frame = 1 
Query:  622 EIACFRWEIKNLLNLRNRNQE-IASGYFFSHCRQYEMWLYFYPKGSEYNDDFQISFRLWI------QSSHKYDSKWPFLGQVTLAIWNSKKPTLQESITVQLNGNISLL-RP----FYRSDPINFSFPKLQISNDFDSL--TSYCSVS 1023
            +IA FRW I NL  +RN   + I S YF+S  R+Y M L+ +P G   N    IS +L +       +++   +K+PF   +T++I NS KP + +SI+      +SLL RP    +  S+  NF++  L +   F +   T  C++S
Sbjct:  302 KIATFRWNIDNLKEIRNDGDDMIYSDYFYSINREYRMRLWVFPNGVGDNLGNDISVQLLVWNNENDVATNNVSTKFPFKADITISIRNSIKPQIYQSIS-----QLSLLDRPNLFLYTTSELFNFNYTHLNLGGVFANQFSTVECAIS 444
[Close]
BLAST of SMED30015116 vs. Planmine SMEST
Match: SMESG000012339.1 (SMESG000012339.1)

HSP 1 Score: 64.3142 bits (155), Expect = 5.485e-11
Identity = 49/148 (33.11%), Postives = 78/148 (52.70%), Query Frame = 1 
Query:  622 EIACFRWEIKNLLNLRNRNQE-IASGYFFSHCRQYEMWLYFYPKGSEYNDDFQISFRLWI------QSSHKYDSKWPFLGQVTLAIWNSKKPTLQESITVQLNGNISLL-RP----FYRSDPINFSFPKLQISNDFDSL--TSYCSVS 1023
            +IA FRW I NL  +RN   + I S YF+S  R+Y M L+ +P G   N    IS +L +       +++   +K+PF   +T++I NS KP + +SI+      +SLL RP    +  S+  NF++  L +   F +   T  C++S
Sbjct:  305 KIATFRWNIDNLKEIRNDGDDMIYSDYFYSINREYRMRLWVFPNGVGDNLGNDISVQLLVWNNENDVATNNVSTKFPFKADITISIRNSIKPQIYQSIS-----QLSLLDRPNLFLYTTSELFNFNYTHLNLGGVFANQFSTVECAIS 447
[Close]
BLAST of SMED30015116 vs. Planmine SMEST
Match: SMESG000012339.1 (SMESG000012339.1)

HSP 1 Score: 64.3142 bits (155), Expect = 5.812e-11
Identity = 49/148 (33.11%), Postives = 78/148 (52.70%), Query Frame = 1 
Query:  622 EIACFRWEIKNLLNLRNRNQE-IASGYFFSHCRQYEMWLYFYPKGSEYNDDFQISFRLWI------QSSHKYDSKWPFLGQVTLAIWNSKKPTLQESITVQLNGNISLL-RP----FYRSDPINFSFPKLQISNDFDSL--TSYCSVS 1023
            +IA FRW I NL  +RN   + I S YF+S  R+Y M L+ +P G   N    IS +L +       +++   +K+PF   +T++I NS KP + +SI+      +SLL RP    +  S+  NF++  L +   F +   T  C++S
Sbjct:  311 KIATFRWNIDNLKEIRNDGDDMIYSDYFYSINREYRMRLWVFPNGVGDNLGNDISVQLLVWNNENDVATNNVSTKFPFKADITISIRNSIKPQIYQSIS-----QLSLLDRPNLFLYTTSELFNFNYTHLNLGGVFANQFSTVECAIS 453
The following BLAST results are available for this feature:
BLAST of SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 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 SMED30015116 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000012426.16.896e-155100.00SMESG000012426.1[more]
SMESG000012426.11.619e-13090.34SMESG000012426.1[more]
SMESG000012339.14.894e-1133.11SMESG000012339.1[more]
SMESG000012339.15.485e-1133.11SMESG000012339.1[more]
SMESG000012339.15.812e-1133.11SMESG000012339.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015116 ID=SMED30015116|Name=SMED30015116|organism=Schmidtea mediterranea sexual|type=transcript|length=1186bp
GTTAAATGTTTATTTAATATTTGGTTTTACAATAACAATCCATTCTATCA
AGTGATTCTATCAATTTAGTTCATTTAAACAATAAATTCCCATTATTATT
TTATTATATAGCATCTATTGAGTTGAAATATATTAAAATGGTAAATTTTA
AAGACATTCAAAAACATTTTAAAATCTCTAAAATTGATAAATCTTTTTGT
GCAATTTGTAATGGACATGTTGGAGATACCCGTGGGGAGTTATGCCAGTG
TTTGTATTGCAAGAATTGTTTAACGAAATTCATGAATTTGAACAAAAACC
TTTTTCATTTAAAAGACTGTAAATTTCATAGACCTTTCAATTCGATTTTT
GAGAAATCGAAGAACTGGTTTATTGAAACTGAAGGAAGACAAAACAAGAA
CATTAAAAGCGAAGCAAGTTTTCTTTGGATATTTATAATTTATTTTTTTT
TAGAATAAAGTCGAAGTTTTCACTAATTTTCAAAGTTATTCTTTAGACAA
TGACAAAAATAAAAAACAAAATGACAAAACTGAAAAATATGATATTTTAA
CTAAACCCAAGGATTTATTTATCCAGTCCACTTCTAAGAGATTGGGGTCG
GGATGGTTTGACAATTCTAATGAGATCGCTTGTTTTCGGTGGGAAATCAA
AAATTTATTGAACTTAAGAAACCGAAACCAAGAAATAGCCAGTGGTTATT
TTTTTTCACACTGCCGGCAATATGAAATGTGGCTGTACTTTTATCCGAAG
GGGTCGGAATACAATGATGATTTTCAAATAAGTTTCCGATTGTGGATTCA
AAGTAGTCACAAATACGATTCTAAATGGCCTTTTCTCGGCCAAGTGACTT
TGGCAATTTGGAATTCGAAAAAACCCACATTACAAGAAAGTATAACAGTA
CAGCTAAATGGTAACATCTCCTTATTGAGACCGTTTTATCGGTCCGATCC
AATAAATTTCAGTTTCCCTAAACTTCAGATTTCCAACGATTTTGATTCAC
TTACTTCATATTGTTCAGTGAGCTGCTGTGAATGAATTCATCCAATTATT
TGCAGTTTCGGTTCAAATATTTTTCAAAAGCAAGTCCCGGGCAGCTACTT
CATTTTCTTGCGTTATGGTACATTGTTTATGGACTTGGATTTTTTTTCTA
AAGAAATTTTTCTTGAAATTAAAATGTGTTCTAAAC
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protein sequence of SMED30015116-orf-1

>SMED30015116-orf-1 ID=SMED30015116-orf-1|Name=SMED30015116-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
MWLYFYPKGSEYNDDFQISFRLWIQSSHKYDSKWPFLGQVTLAIWNSKKP
TLQESITVQLNGNISLLRPFYRSDPINFSFPKLQISNDFDSLTSYCSVSC
CE*
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protein sequence of SMED30015116-orf-2

>SMED30015116-orf-2 ID=SMED30015116-orf-2|Name=SMED30015116-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp
MVNFKDIQKHFKISKIDKSFCAICNGHVGDTRGELCQCLYCKNCLTKFMN
LNKNLFHLKDCKFHRPFNSIFEKSKNWFIETEGRQNKNIKSEASFLWIFI
IYFFLE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR008974TRAF-like
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding