SMED30027562

Overview
NameSMED30027562
Smed IDSMED30027562
Length (bp)715
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 SMED30027562 (SMED30027562) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027562 (SMED30027562) 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 SMED30027562 (SMED30027562) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027562 (SMED30027562) 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



SMED30027562

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30027562SMESG000022880.1 SmedASXL_010716SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
protonephridiaSMED30027562SMESG000022880.1 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30027562SMESG000022880.1 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30027562SMESG000022880.1 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30027562SMESG000022880.1 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30027562SMESG000022880.1 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30027562SMESG000022880.1 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027562SMESG000022880.1 SMESG000029463.1 Contig40809newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027562SMESG000022880.1 SMESG000029463.1 Contig40809uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
zeta neoblastSMED30027562SMESG000022880.1 dd_Smed_v4_3493_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
SMED30027562 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001230:1396..2268 +3335
Homology
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BLAST of SMED30027562 vs. TrEMBL
Match: A0A5J4NWQ9 (HMG box domain-containing protein OS=Paragonimus westermani OX=34504 GN=DEA37_0013666 PE=4 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 7.640e-8
Identity = 29/88 (32.95%), Postives = 48/88 (54.55%), Query Frame = 1 
Query:  316 IKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTN 579
            +++A +HG+P+K   S LNVY++E   + +     K+  KL+  V ++K+L+ SE   Y  K    KA YE  ++ W    D+ F  N
Sbjct:  137 VQYAHKHGMPRKPPISGLNVYIREKLCDLKGQSITKVATKLRDAVQNWKSLSPSEQATYGLKAQQLKAAYEKELEAWASEHDLRFTRN 224
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BLAST of SMED30027562 vs. TrEMBL
Match: A0A4E0RQF0 (HMG box domain-containing protein OS=Fasciola hepatica OX=6192 GN=D915_001227 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 1.567e-6
Identity = 28/96 (29.17%), Postives = 54/96 (56.25%), Query Frame = 1 
Query:  292 AETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTN 579
            A +++ + + +A  HG+P+K   S LNVY+QE  ++ +     K+  +L+  V D+  L++ E ++Y+ K +  KA+YE  ++ W     + F  N
Sbjct:   94 AWSEKQKSLMYAHRHGMPRKPPASGLNVYIQEKLSDLKGMSLNKVTLRLRDAVKDWNALSEDERKIYSAKATELKAEYEKELQSWATEHKLRFTKN 189
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BLAST of SMED30027562 vs. TrEMBL
Match: A0A504YQ35 (HMG box domain-containing protein OS=Fasciola gigantica OX=46835 GN=FGIG_03396 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 2.476e-6
Identity = 28/96 (29.17%), Postives = 54/96 (56.25%), Query Frame = 1 
Query:  292 AETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTN 579
            A +++ + + +A  HG+P+K   S LNVY+QE  ++ +     K+  +L+  V D+  L++ E ++Y+ K +  KA+YE  ++ W     + F  N
Sbjct:  122 AWSEKRKSLMYAHRHGMPRKPPASGLNVYIQEKLSDLKGMSLNKVTLRLRDAVKDWNALSEDERKIYSAKATELKAEYEKELQSWATEHKLRFTKN 217
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BLAST of SMED30027562 vs. Planmine SMEST
Match: SMESG000022880.1 (SMESG000022880.1)

HSP 1 Score: 360.533 bits (924), Expect = 6.450e-128
Identity = 189/191 (98.95%), Postives = 190/191 (99.48%), Query Frame = 1 
Query:   22 MQRKIINTILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKKTLMNVVRDQFKSLSGXXXXXXXXXXRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTNRRKVA 594
            MQRKIINTILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKKTLMNVVRDQFKSLSGEEKKELEEKLRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSE+QVYNDKFSAFK DYETLMKEWTKAKDVPFLTNRRKVA
Sbjct:    1 MQRKIINTILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKKTLMNVVRDQFKSLSGEEKKELEEKLRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSELQVYNDKFSAFKTDYETLMKEWTKAKDVPFLTNRRKVA 191
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BLAST of SMED30027562 vs. Planmine SMEST
Match: SMESG000022878.1 (SMESG000022878.1)

HSP 1 Score: 93.2041 bits (230), Expect = 3.990e-23
Identity = 54/184 (29.35%), Postives = 106/184 (57.61%), Query Frame = 1 
Query:   43 TILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKKTLMNVVRDQFKSLSGXXXXXXXXXXRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTNRRKVA 594
            + +R +SKI  +KPP S++ ++ R N  K +S     +   ++++++    +++K LS  E + L+  L+I N +Y+++  + +  K  +II FAE++G+PK+   S LN++++E        P +  + +   +V D+KNL  +E+  YN++F   K ++   MKEW     +PF  NR+++A
Sbjct:    7 SFIRKISKIKLDKPPASVFGMFLRLNNSKHQSGNNNKSDITNRRSML----EKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIVRYNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLA 186
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BLAST of SMED30027562 vs. Planmine SMEST
Match: SMESG000022878.1 (SMESG000022878.1)

HSP 1 Score: 76.6406 bits (187), Expect = 4.259e-17
Identity = 42/133 (31.58%), Postives = 78/133 (58.65%), Query Frame = 1 
Query:  196 DQFKSLSGXXXXXXXXXXRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTNRRKVA 594
            +++K LS  E + L+  L+I N +Y+++  + +  K  +II FAE++G+PK+   S LN++++E        P +  + +   +V D+KNL  +E+  YN++F   K ++   MKEW     +PF  NR+++A
Sbjct:   28 EKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIVRYNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLA 160
The following BLAST results are available for this feature:
BLAST of SMED30027562 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 SMED30027562 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 SMED30027562 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 SMED30027562 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 SMED30027562 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 SMED30027562 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 SMED30027562 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 SMED30027562 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A5J4NWQ97.640e-832.95HMG box domain-containing protein OS=Paragonimus w... [more]
A0A4E0RQF01.567e-629.17HMG box domain-containing protein OS=Fasciola hepa... [more]
A0A504YQ352.476e-629.17HMG box domain-containing protein OS=Fasciola giga... [more]
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BLAST of SMED30027562 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 SMED30027562 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 SMED30027562 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 SMED30027562 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 SMED30027562 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 SMED30027562 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000022880.16.450e-12898.95SMESG000022880.1[more]
SMESG000022878.13.990e-2329.35SMESG000022878.1[more]
SMESG000022878.14.259e-1731.58SMESG000022878.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027562 ID=SMED30027562|Name=SMED30027562|organism=Schmidtea mediterranea sexual|type=transcript|length=715bp
ATCTATATAAATCTTATATGAATGCAAAGAAAAATTATAAATACCATTTT
GAGAGGAGTTTCGAAAATAGCTTTTGAAAAGCCACCAAATTCAATTTATT
TTTTATACTTTCGTGAAAACTATTTAAAATTAAAGTCTGAAACGGAATTT
AATAATTTGCCTTTTGACAAAAAGACATTAATGAATGTGGTTAGAGATCA
ATTTAAAAGTTTATCAGGGGAAGAAAAAAAAGAACTTGAAGAAAAGTTAA
GAATAGTTAATGAAGATTATATCAAGATGAAAAATATGGAAGCTGAAACT
AAAGAATCGGAAATTATAAAATTTGCAGAAGAACACGGGTTGCCAAAAAA
AACTGTAACATCTGCTCTTAATGTGTATGTACAAGAAATATTTGCAAATA
AAGAAATTTATCCTGAGTTAAAAATACAAGATAAACTTAAGCAAGTTGTT
CATGATTTCAAAAATTTAACTGATTCAGAGATGCAGGTTTACAACGATAA
ATTTTCTGCATTCAAAGCAGATTACGAAACGTTAATGAAAGAATGGACAA
AGGCAAAAGATGTTCCATTTTTAACTAATAGGAGGAAAGTTGCATTTTAC
TTTTACTATAAAGAGAAATATAACAAATGAAATTGTCTTGTATATTATAT
GATGTTAGATGTTAAGCTGATATTTAATTAGATTTCGATAAATATATTTG
TTTTATTAAAAAAAA
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protein sequence of SMED30027562-orf-1

>SMED30027562-orf-1 ID=SMED30027562-orf-1|Name=SMED30027562-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=203bp
MQRKIINTILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDK
KTLMNVVRDQFKSLSGEEKKELEEKLRIVNEDYIKMKNMEAETKESEIIK
FAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLT
DSEMQVYNDKFSAFKADYETLMKEWTKAKDVPFLTNRRKVAFYFYYKEKY
NK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR036910HMG_box_dom_sf
IPR009071HMG_box_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 69..89
NoneNo IPR availablePANTHERPTHR46597FAMILY NOT NAMEDcoord: 20..177
IPR036910High mobility group box domain superfamilyGENE3DG3DSA:1.10.30.10coord: 15..104
e-value: 5.7E-7
score: 31.7
IPR036910High mobility group box domain superfamilyGENE3DG3DSA:1.10.30.10coord: 105..190
e-value: 3.8E-9
score: 38.8
IPR036910High mobility group box domain superfamilySUPERFAMILYSSF47095HMG-boxcoord: 19..85
IPR036910High mobility group box domain superfamilySUPERFAMILYSSF47095HMG-boxcoord: 105..178