SMED30020374

Overview
NameSMED30020374
Smed IDSMED30020374
Length (bp)1286
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 SMED30020374 (SMED30020374) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020374 (SMED30020374) 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 SMED30020374 (SMED30020374) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020374 (SMED30020374) 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



SMED30020374

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30020374SMESG000036052.1 SMESG000036051.1 dd_Smed_v4_6701_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020374SMESG000036052.1 SMESG000036051.1 dd_Smed_v4_6701_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020374SMESG000036052.1 SMESG000036051.1 dd_Smed_v4_6701_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020374SMESG000036052.1 SMESG000036051.1 dd_Smed_v4_6701_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
[Close]
BLAST of SMED30020374 vs. Planmine SMEST
Match: SMESG000036051.1 (SMESG000036051.1)

HSP 1 Score: 353.984 bits (907), Expect = 3.920e-121
Identity = 177/186 (95.16%), Postives = 178/186 (95.70%), Query Frame = 2 
Query:  167 GTSDKSETVKSTGIVNSNDTDISESVTFNNGSNIGTGTETSQDILHSIPKRSSNNYEGINSSRNIEEGIGNKNSLEINVAVKCIESGNNPQEPRNIPLMTEQEKSTMENNENQPKAESHTSPKLKKS---FLDSFSNCYFGYFLIRCFGKFLIRIKYPLNIILGLLNKSGIFNWTSGVISHFQQNA 715
             TSDKSETVKSTGIVNSNDTDISES TFNNGSNIGTGT TSQDILHSIPKRSSNNYEGINSSRNIE GIGNKNSLEINVAVKCIESGNNPQEPRNIPLMTEQEKS+MENNENQPKAESHTSPKLKKS   FLDSF NCYFGYFLIRCFGKFLIRIKYPLNIILGLLNKSGIFNWTSGVISHFQQNA
Sbjct:  100 ATSDKSETVKSTGIVNSNDTDISESGTFNNGSNIGTGTTTSQDILHSIPKRSSNNYEGINSSRNIE-GIGNKNSLEINVAVKCIESGNNPQEPRNIPLMTEQEKSSMENNENQPKAESHTSPKLKKSKKSFLDSFFNCYFGYFLIRCFGKFLIRIKYPLNIILGLLNKSGIFNWTSGVISHFQQNA 284

HSP 2 Score: 57.3806 bits (137), Expect = 5.859e-9
Identity = 54/84 (64.29%), Postives = 60/84 (71.43%), Query Frame = 2 
Query:   92 MSENSSVNDGVXXXXXXXXXXXXXXGTSDKSETVKSTGIVNSNDTDISESVTFNNGSNIG-----------TGTETSQDILHSI 310
            MSENSSVNDGVEENSQENEENKSKNGT+DKSE    T I ++NDT ISES TFNNGSN             TGT   QD+++SI
Sbjct:    1 MSENSSVNDGVEENSQENEENKSKNGTNDKSEIEMLTVIASANDTHISESDTFNNGSNFNLDRNPSSENNETGTAPIQDLINSI 84
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BLAST of SMED30020374 vs. Planmine SMEST
Match: SMESG000036052.1 (SMESG000036052.1)

HSP 1 Score: 244.973 bits (624), Expect = 2.455e-79
Identity = 119/120 (99.17%), Postives = 120/120 (100.00%), Query Frame = 2 
Query:  719 LFDLIKALRNSDESALNEALKTVQKYVTESSLGDDVYKCFMNILSRVSTVLKATHTETSNLHATLSDKAQGNFEKFKKETPGFVFDNFYGQLAFHMTCNVCQQIFNESFQVLKSISLALP 1078
            LFDLIKALRNSDESALNEALKTVQKYVTESSLGDDVYKCFMNILSRVSTVLKATHTETSNLHATLSDKAQGNFEKFKKETPGFVFDNFYGQLAFHMTCNVCQQIFNESFQVLKSISLA+P
Sbjct:   49 LFDLIKALRNSDESALNEALKTVQKYVTESSLGDDVYKCFMNILSRVSTVLKATHTETSNLHATLSDKAQGNFEKFKKETPGFVFDNFYGQLAFHMTCNVCQQIFNESFQVLKSISLAVP 168
[Close]
BLAST of SMED30020374 vs. Planmine SMEST
Match: SMESG000036051.1 (SMESG000036051.1)

HSP 1 Score: 240.35 bits (612), Expect = 2.661e-77
Identity = 122/127 (96.06%), Postives = 123/127 (96.85%), Query Frame = 2 
Query:  167 GTSDKSETVKSTGIVNSNDTDISESVTFNNGSNIGTGTETSQDILHSIPKRSSNNYEGINSSRNIEEGIGNKNSLEINVAVKCIESGNNPQEPRNIPLMTEQEKSTMENNENQPKAESHTSPKLKKS 547
             TSDKSETVKSTGIVNSNDTDISES TFNNGSNIGTGT TSQDILHSIPKRSSNNYEGINSSRNI EGIGNKNSLEINVAVKCIESGNNPQEPRNIPLMTEQEKS+MENNENQPKAESHTSPKLKKS
Sbjct:  100 ATSDKSETVKSTGIVNSNDTDISESGTFNNGSNIGTGTTTSQDILHSIPKRSSNNYEGINSSRNI-EGIGNKNSLEINVAVKCIESGNNPQEPRNIPLMTEQEKSSMENNENQPKAESHTSPKLKKS 225

HSP 2 Score: 56.225 bits (134), Expect = 8.424e-9
Identity = 54/84 (64.29%), Postives = 60/84 (71.43%), Query Frame = 2 
Query:   92 MSENSSVNDGVXXXXXXXXXXXXXXGTSDKSETVKSTGIVNSNDTDISESVTFNNGSNIG-----------TGTETSQDILHSI 310
            MSENSSVNDGVEENSQENEENKSKNGT+DKSE    T I ++NDT ISES TFNNGSN             TGT   QD+++SI
Sbjct:    1 MSENSSVNDGVEENSQENEENKSKNGTNDKSEIEMLTVIASANDTHISESDTFNNGSNFNLDRNPSSENNETGTAPIQDLINSI 84
[Close]
BLAST of SMED30020374 vs. Planmine SMEST
Match: SMESG000036052.1 (SMESG000036052.1)

HSP 1 Score: 234.572 bits (597), Expect = 4.535e-75
Identity = 119/138 (86.23%), Postives = 120/138 (86.96%), Query Frame = 2 
Query:  719 LFDLIKALRNSDESALNEALKTVQKYVTESSLG------------------DDVYKCFMNILSRVSTVLKATHTETSNLHATLSDKAQGNFEKFKKETPGFVFDNFYGQLAFHMTCNVCQQIFNESFQVLKSISLALP 1078
            LFDLIKALRNSDESALNEALKTVQKYVTESSLG                  DDVYKCFMNILSRVSTVLKATHTETSNLHATLSDKAQGNFEKFKKETPGFVFDNFYGQLAFHMTCNVCQQIFNESFQVLKSISLA+P
Sbjct:   49 LFDLIKALRNSDESALNEALKTVQKYVTESSLGSFDRIQCLTLTSYNSNSSDDVYKCFMNILSRVSTVLKATHTETSNLHATLSDKAQGNFEKFKKETPGFVFDNFYGQLAFHMTCNVCQQIFNESFQVLKSISLAVP 186
[Close]
BLAST of SMED30020374 vs. Planmine SMEST
Match: SMESG000036051.1 (SMESG000036051.1)

HSP 1 Score: 189.119 bits (479), Expect = 6.285e-58
Identity = 98/105 (93.33%), Postives = 99/105 (94.29%), Query Frame = 2 
Query:  167 GTSDKSETVKSTGIVNSNDTDISESVTFNNGSNIGTGTETSQDILHSIPKRSSNNYEGINSSRNIEEGIGNKNSLEINVAVKCIESGNNPQEPRNIPLMTEQEKS 481
             TSDKSETVKSTGIVNSNDTDISES TFNNGSNIGTGT TSQDILHSIPKRSSNNYEGINSSRNI EGIGNKNSLEINVAVKCIESGNNPQEPRNIPLMTE  +S
Sbjct:  100 ATSDKSETVKSTGIVNSNDTDISESGTFNNGSNIGTGTTTSQDILHSIPKRSSNNYEGINSSRNI-EGIGNKNSLEINVAVKCIESGNNPQEPRNIPLMTEPTES 203

HSP 2 Score: 55.4546 bits (132), Expect = 9.642e-9
Identity = 54/84 (64.29%), Postives = 60/84 (71.43%), Query Frame = 2 
Query:   92 MSENSSVNDGVXXXXXXXXXXXXXXGTSDKSETVKSTGIVNSNDTDISESVTFNNGSNIG-----------TGTETSQDILHSI 310
            MSENSSVNDGVEENSQENEENKSKNGT+DKSE    T I ++NDT ISES TFNNGSN             TGT   QD+++SI
Sbjct:    1 MSENSSVNDGVEENSQENEENKSKNGTNDKSEIEMLTVIASANDTHISESDTFNNGSNFNLDRNPSSENNETGTAPIQDLINSI 84
The following BLAST results are available for this feature:
BLAST of SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 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 SMED30020374 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000036051.13.920e-12195.16SMESG000036051.1[more]
SMESG000036052.12.455e-7999.17SMESG000036052.1[more]
SMESG000036051.12.661e-7796.06SMESG000036051.1[more]
SMESG000036052.14.535e-7586.23SMESG000036052.1[more]
SMESG000036051.16.285e-5893.33SMESG000036051.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020374 ID=SMED30020374|Name=SMED30020374|organism=Schmidtea mediterranea sexual|type=transcript|length=1286bp
CTTGAATATTTTAATATTCATTTTAATATTTTCATTTTGAATTCTTCATA
ATTTTATAACTGATTTTATAAATATTAGGCTAGTGAAAAATATGTCCGAA
AATTCAAGTGTCAATGACGGAGTTGAAGAAAATTCTCAAGAAAATGAAGA
AAATAAAAGCAAAAATGGGACGAGTGATAAAAGTGAAACTGTAAAGTCAA
CAGGTATTGTCAATTCAAATGATACTGATATATCTGAATCTGTTACCTTC
AATAACGGATCAAATATCGGAACTGGAACTGAAACGAGTCAAGATATATT
ACATTCAATCCCAAAAAGGAGTTCTAATAACTACGAAGGAATTAATTCTA
GTAGAAACATAGAAGAAGGGATTGGAAATAAAAATTCATTGGAAATAAAT
GTAGCAGTAAAATGTATCGAAAGTGGAAATAATCCACAGGAACCTCGAAA
TATTCCATTGATGACCGAACAGGAAAAATCTACTATGGAAAACAATGAAA
ACCAACCGAAAGCTGAATCTCATACTTCACCAAAATTAAAAAAGTCATTT
TTAGACAGCTTTTCTAATTGTTATTTTGGCTATTTTCTTATTCGTTGTTT
TGGCAAATTTCTTATTAGAATAAAATATCCTTTGAATATCATTCTGGGTT
TACTGAATAAATCTGGTATCTTCAATTGGACAAGTGGAGTTATTTCTCAT
TTTCAACAAAATGCATGTCTATTCGATTTGATAAAAGCTTTAAGAAACTC
AGATGAATCCGCGCTTAACGAAGCTTTAAAAACTGTTCAAAAATATGTTA
CGGAGTCGTCTCTCGGTGATGACGTGTACAAGTGTTTCATGAATATTCTA
AGTCGAGTGAGCACAGTTCTAAAAGCAACCCACACTGAAACGTCAAATCT
TCACGCGACTCTTTCTGATAAAGCTCAAGGAAATTTCGAAAAATTCAAAA
AGGAAACCCCCGGATTTGTGTTCGATAATTTTTATGGCCAATTGGCATTC
CATATGACCTGTAATGTTTGTCAGCAAATATTCAACGAGTCCTTCCAAGT
GCTGAAATCTATTTCACTGGCTTTACCTAGGACCATACTCTACAGTTGTC
AGAAAAATTCCAAATAGACGTTCCAAGACACCAAGACAAGACAGTCCAGC
AACAACAACGAGCTTTGGAATTCGGAAAGTGAATACGCTTCCAGCATATG
CTGCAGTTCTCTGTATAAATGATGTTAGGGTATCGATATCTGCAAATGAT
AATCGATAAGCTGCATCATTTAATAATTTATTGGCG
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protein sequence of SMED30020374-orf-1

>SMED30020374-orf-1 ID=SMED30020374-orf-1|Name=SMED30020374-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=342bp
MSENSSVNDGVEENSQENEENKSKNGTSDKSETVKSTGIVNSNDTDISES
VTFNNGSNIGTGTETSQDILHSIPKRSSNNYEGINSSRNIEEGIGNKNSL
EINVAVKCIESGNNPQEPRNIPLMTEQEKSTMENNENQPKAESHTSPKLK
KSFLDSFSNCYFGYFLIRCFGKFLIRIKYPLNIILGLLNKSGIFNWTSGV
ISHFQQNACLFDLIKALRNSDESALNEALKTVQKYVTESSLGDDVYKCFM
NILSRVSTVLKATHTETSNLHATLSDKAQGNFEKFKKETPGFVFDNFYGQ
LAFHMTCNVCQQIFNESFQVLKSISLALPRTILYSCQKNSK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000418head
PLANA:0002032epidermal cell