SMED30010160

Overview
NameSMED30010160
Smed IDSMED30010160
Length (bp)2553
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 SMED30010160 (SMED30010160) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010160 (SMED30010160) 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 SMED30010160 (SMED30010160) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010160 (SMED30010160) 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




SMED30010160

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30010160SMESG000039545.1 SmedASXL_016399SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
epidermal cellSMED30010160SMESG000039545.1 dd_Smed_v4_6115_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30010160SMESG000039545.1 dd_Smed_v6_6115_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30010160SMESG000039545.1 dd_Smed_v4_6115_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30010160SMESG000039545.1 dd_Smed_v4_6115_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30010160SMESG000039545.1 dd_Smed_v4_6115_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30010160SMESG000039545.1 dd_Smed_v4_6115_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
SMED30010160 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002122:52077..56765 -12705
Homology
BLAST of SMED30010160 vs. Planmine SMEST
Match: SMESG000039545.1 (SMESG000039545.1)

HSP 1 Score: 1576.99 bits (4082), Expect = 0.000e+0
Identity = 795/828 (96.01%), Postives = 801/828 (96.74%), Query Frame = 3
Query:   24 CWDNKGIIGQEISEETKEGRSNKGLDYGNVYIVKSSDINANLQNEIIPNVEYIADQDNEEKIIMNNKIKCENDIETVNKTEELQQKNTDYQYYEPKFQDIDNCRVNSTESNPIFLSDNEENSLSKKLLQINQEPFPLIVDCLESEIIPTGAKSQFYQPESAKSFSNNLNTVESVFANYLTDGDYWSSGRNPICDIQSNSPNSSPAEEGVFSENNKDRKINFNSENLNQIYSRENSQLSNNIEEAPLQIFNNYDDNNDKFSERKFSSSDNITEKNDCESSMEINSNKSDRISNRNTQIFSPANLSFPKNMEVKQNPKSKNKLYEKNVVNNKASKENHVSAVTEKENENERFSYKTLTPSKFEILSEKIHNNMNKYDFEKPANRNHPATQDNNQSEFESTRKLSNREFSLKQSNNPNKTISSTENFDSKSFSSREWLKENPNWDNYEKEKSKTHSMSLFGSSQRSFSNLENQSNSEKYYSALDSIPSFVNSREIKQNNVSNSKSPTGNYNRSSISLENDSYKYSLAFPEPRLYNYKDPHQETLQSKFFINESSDKWKFSSETPYSNKLRTNIEFGTKSMDLNNLTNFRKNRDNIAKASKSSCYQTPTFLTKGSSTKYSDSFYEVSDLNYIKSSKHYDLEPQEIGFDRNQKKYLYTKSNNNERFNDYQGLNSFDCISNYRNLKFSSTRINSDSNRQNERGSTEKDDFRKIYRFEDTMNPQFCKKCMRFHSSSKLKQSECKSSSNVDIFKKENSRSLLRTIDSTTNNFLPKNKFVNKIPSRKEKESFTRPQYHFEDHDYSESYSKPDTSDAGSNSPLAFRVYCRGRLIYEPY 2507
            CWDNKGIIGQEISEETKEGRSNKGLDYGNVYIVKSSDINANLQNEIIPNVEYIADQDNEEKIIMNNKIKCENDIETVNKTEELQQKNTDYQYYEPKFQDIDNCRVNSTESNPIFLSDNEENSLSKKLLQINQEPFPLIVDCLESEIIPTGAKSQFYQPESAKSFSNNLNTVESVFANYLTDGDYWSSGRNPICDIQSNSPNSSPA+EGVFSENNKDRKINFNSENLNQIYSRENSQLSNNIEEAPLQIFNNYDDNNDKFSERKFSSSDNITEKNDCESSMEINSNKSDRI       FSPANLSF KN+EV+QNPKSKNKLYEKNVVNNKASKENHVSAVTEKENENERFSYKTLTPSKFEILSEKIHNNMNKYDFEKPANRNHPATQDNNQSEFE+TRKLSNREFSLKQSN PNKTI STENFDSKSFSSREWLKENPNWDNYEKEKSKTHSMSLFGSSQRSFSNLENQSNSEKYYSALDSIPSFVNSREIKQNNVSNSKSPTGNYNRSSISLENDSYKYSLAFPEPRLYNYKDPHQETLQSKFFINESSDKWKFSSETPYSNKLRTNIEFGTKSMDLNNLTNFRKNRDNIAKASKSSCYQTPTFLTKGSSTKYSDSFYEVSDLNYIKSSKHYDLEPQEIGFDRNQKKYLYTKSNNNE                 RNLKFSSTRINSDSNRQNERGSTEKDDFRKIYRFEDTMNPQFCKKCMRFHSSSKLKQSECKSSSNVDIFKKENSRSLLRTIDSTTNNFLPKNKFVNKIP+RKEKESFTRPQYHFEDHDYSESYSKPDTSD+GSNSPLAFRVYCRGRLIYEPY
Sbjct:  662 CWDNKGIIGQEISEETKEGRSNKGLDYGNVYIVKSSDINANLQNEIIPNVEYIADQDNEEKIIMNNKIKCENDIETVNKTEELQQKNTDYQYYEPKFQDIDNCRVNSTESNPIFLSDNEENSLSKKLLQINQEPFPLIVDCLESEIIPTGAKSQFYQPESAKSFSNNLNTVESVFANYLTDGDYWSSGRNPICDIQSNSPNSSPAKEGVFSENNKDRKINFNSENLNQIYSRENSQLSNNIEEAPLQIFNNYDDNNDKFSERKFSSSDNITEKNDCESSMEINSNKSDRI-------FSPANLSFSKNIEVEQNPKSKNKLYEKNVVNNKASKENHVSAVTEKENENERFSYKTLTPSKFEILSEKIHNNMNKYDFEKPANRNHPATQDNNQSEFETTRKLSNREFSLKQSNYPNKTIYSTENFDSKSFSSREWLKENPNWDNYEKEKSKTHSMSLFGSSQRSFSNLENQSNSEKYYSALDSIPSFVNSREIKQNNVSNSKSPTGNYNRSSISLENDSYKYSLAFPEPRLYNYKDPHQETLQSKFFINESSDKWKFSSETPYSNKLRTNIEFGTKSMDLNNLTNFRKNRDNIAKASKSSCYQTPTFLTKGSSTKYSDSFYEVSDLNYIKSSKHYDLEPQEIGFDRNQKKYLYTKSNNNE-----------------RNLKFSSTRINSDSNRQNERGSTEKDDFRKIYRFEDTMNPQFCKKCMRFHSSSKLKQSECKSSSNVDIFKKENSRSLLRTIDSTTNNFLPKNKFVNKIPNRKEKESFTRPQYHFEDHDYSESYSKPDTSDSGSNSPLAFRVYCRGRLIYEPY 1465          
The following BLAST results are available for this feature:
BLAST of SMED30010160 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 SMED30010160 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 SMED30010160 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 SMED30010160 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 SMED30010160 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 SMED30010160 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 SMED30010160 vs. UniProt
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 SMED30010160 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 SMED30010160 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 SMED30010160 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 SMED30010160 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 SMED30010160 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 SMED30010160 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 SMED30010160 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000039545.10.000e+096.01SMESG000039545.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010160 ID=SMED30010160|Name=SMED30010160|organism=Schmidtea mediterranea sexual|type=transcript|length=2553bp
ATAATAATAATAATAATAATAACTGCTGGGATAATAAAGGCATTATTGGG
CAAGAAATAAGTGAGGAGACTAAAGAAGGAAGATCCAATAAAGGTCTTGA
CTATGGAAATGTGTATATTGTGAAGAGCTCAGATATAAATGCCAACTTAC
AAAATGAAATAATTCCAAATGTTGAGTATATTGCGGATCAAGACAATGAA
GAAAAAATAATAATGAATAACAAAATTAAATGTGAAAATGACATTGAAAC
TGTGAACAAGACTGAAGAATTGCAACAGAAAAATACCGACTACCAATATT
ATGAGCCAAAGTTTCAAGATATTGACAATTGCAGAGTAAATAGCACTGAA
AGTAACCCGATTTTTCTGAGCGATAATGAAGAAAATTCATTAAGCAAGAA
ATTACTACAAATTAATCAAGAACCTTTTCCATTAATTGTTGATTGTTTAG
AATCTGAAATTATTCCGACTGGTGCAAAGTCTCAATTTTATCAACCGGAA
AGTGCAAAATCGTTTTCTAATAACCTTAATACTGTTGAATCTGTTTTCGC
AAATTATTTGACTGACGGCGATTATTGGAGTTCCGGTCGCAATCCGATTT
GCGATATCCAATCAAATTCTCCCAATTCAAGTCCAGCTGAAGAAGGTGTT
TTTTCGGAAAATAATAAAGATAGAAAAATTAATTTTAATTCTGAAAATTT
AAATCAAATTTATTCTAGAGAAAATAGTCAATTGTCTAATAATATAGAAG
AAGCACCATTACAAATATTTAATAATTATGATGATAACAATGATAAATTT
TCTGAACGGAAATTCAGTTCATCTGATAATATCACCGAAAAGAACGATTG
TGAAAGCTCAATGGAGATAAACAGCAACAAATCTGATAGAATATCTAATA
GAAATACTCAAATATTTAGCCCCGCAAATCTTTCTTTTCCAAAAAATATG
GAAGTAAAACAAAATCCCAAATCAAAAAATAAATTATACGAAAAAAACGT
GGTTAATAACAAAGCTAGTAAAGAGAATCACGTTTCGGCCGTTACTGAAA
AAGAAAATGAAAATGAGAGATTTAGCTACAAAACTTTAACTCCCTCTAAA
TTTGAAATTCTATCTGAAAAAATTCATAATAATATGAATAAATATGATTT
TGAAAAACCAGCCAATAGAAATCATCCGGCAACTCAAGATAACAATCAAT
CAGAATTCGAAAGCACCCGAAAACTTAGTAATAGAGAATTTTCTTTAAAG
CAATCAAATAATCCTAATAAAACGATTTCTTCTACAGAAAACTTTGATTC
AAAATCATTTTCCTCGCGAGAATGGCTAAAGGAAAATCCAAATTGGGATA
ATTATGAAAAAGAAAAATCAAAAACTCACTCAATGTCCCTATTTGGGAGT
TCTCAGAGAAGTTTTTCAAATCTCGAAAATCAAAGTAATTCAGAAAAATA
TTATTCAGCATTAGATTCGATTCCATCATTTGTGAATTCAAGAGAAATAA
AACAAAATAATGTTTCAAATAGCAAATCACCTACAGGTAATTATAACCGT
TCCAGTATTTCTCTAGAAAATGACAGTTATAAATATTCTTTGGCATTTCC
TGAACCCAGACTCTATAATTATAAAGACCCTCATCAAGAAACTTTGCAAT
CTAAATTCTTCATAAATGAAAGTTCTGATAAGTGGAAATTCTCGTCGGAG
ACTCCTTATTCTAATAAACTTAGAACAAATATTGAGTTTGGTACTAAAAG
CATGGATTTAAATAATCTCACGAACTTCAGAAAGAATCGTGATAACATTG
CTAAAGCTTCAAAATCTTCTTGTTATCAAACGCCAACGTTTCTAACGAAA
GGTTCATCTACAAAATATAGCGATTCATTTTATGAAGTTTCCGATCTGAA
TTATATTAAGTCTTCAAAACATTATGATTTGGAACCTCAAGAAATTGGTT
TTGACCGAAATCAAAAGAAATATTTATATACAAAATCAAACAACAATGAA
AGGTTTAATGACTACCAAGGATTGAATTCTTTTGATTGTATTTCTAATTA
TAGGAACTTGAAATTTTCGAGTACTAGAATAAATTCTGATTCAAACAGGC
AAAATGAAAGAGGTTCGACAGAAAAGGATGATTTTCGTAAAATATATCGT
TTTGAAGATACTATGAATCCACAGTTTTGTAAGAAATGTATGAGATTTCA
TTCTTCCTCAAAACTTAAACAATCGGAATGCAAGTCAAGTTCAAACGTGG
ATATTTTTAAAAAGGAGAATTCTCGAAGCCTTTTAAGAACAATTGATTCA
ACAACCAACAATTTTTTGCCAAAAAATAAGTTTGTAAATAAAATTCCAAG
CAGAAAAGAAAAAGAATCATTCACCAGGCCGCAATATCATTTTGAAGACC
ATGATTATTCAGAATCATATTCAAAACCGGATACTAGTGATGCAGGAAGT
AACTCACCTTTGGCCTTTCGAGTCTATTGCAGAGGAAGATTAATATACGA
ACCTTATTGAGATGAACTAAAACTTATTTTGAATAAAATAATTAGTTTTT
TGG
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protein sequence of SMED30010160-orf-1

>SMED30010160-orf-1 ID=SMED30010160-orf-1|Name=SMED30010160-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=836bp
NNNNNNNCWDNKGIIGQEISEETKEGRSNKGLDYGNVYIVKSSDINANLQ
NEIIPNVEYIADQDNEEKIIMNNKIKCENDIETVNKTEELQQKNTDYQYY
EPKFQDIDNCRVNSTESNPIFLSDNEENSLSKKLLQINQEPFPLIVDCLE
SEIIPTGAKSQFYQPESAKSFSNNLNTVESVFANYLTDGDYWSSGRNPIC
DIQSNSPNSSPAEEGVFSENNKDRKINFNSENLNQIYSRENSQLSNNIEE
APLQIFNNYDDNNDKFSERKFSSSDNITEKNDCESSMEINSNKSDRISNR
NTQIFSPANLSFPKNMEVKQNPKSKNKLYEKNVVNNKASKENHVSAVTEK
ENENERFSYKTLTPSKFEILSEKIHNNMNKYDFEKPANRNHPATQDNNQS
EFESTRKLSNREFSLKQSNNPNKTISSTENFDSKSFSSREWLKENPNWDN
YEKEKSKTHSMSLFGSSQRSFSNLENQSNSEKYYSALDSIPSFVNSREIK
QNNVSNSKSPTGNYNRSSISLENDSYKYSLAFPEPRLYNYKDPHQETLQS
KFFINESSDKWKFSSETPYSNKLRTNIEFGTKSMDLNNLTNFRKNRDNIA
KASKSSCYQTPTFLTKGSSTKYSDSFYEVSDLNYIKSSKHYDLEPQEIGF
DRNQKKYLYTKSNNNERFNDYQGLNSFDCISNYRNLKFSSTRINSDSNRQ
NERGSTEKDDFRKIYRFEDTMNPQFCKKCMRFHSSSKLKQSECKSSSNVD
IFKKENSRSLLRTIDSTTNNFLPKNKFVNKIPSRKEKESFTRPQYHFEDH
DYSESYSKPDTSDAGSNSPLAFRVYCRGRLIYEPY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000096ventral epidermis
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0002032epidermal cell