SMED30023748

Overview
NameSMED30023748
Smed IDSMED30023748
Length (bp)2347
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 SMED30023748 (SMED30023748) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023748 (SMED30023748) 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 SMED30023748 (SMED30023748) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023748 (SMED30023748) 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




SMED30023748

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
headSMED30023748SMESG000022731.1 SmedASXL_007481SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30023748SMESG000022731.1 dd_Smed_v4_13297_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30023748SMESG000022731.1 dd_Smed_v6_13297_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30023748SMESG000022731.1 dd_Smed_v4_13297_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
SMED30023748 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001411:34837..43736 +11684
Homology
BLAST of SMED30023748 vs. Planmine SMEST
Match: SMESG000022731.1 (SMESG000022731.1)

HSP 1 Score: 1266.14 bits (3275), Expect = 0.000e+0
Identity = 711/711 (100.00%), Postives = 711/711 (100.00%), Query Frame = 1
Query:   85 MVCKINFDYEILLXXXXXXXXXXXXXXXXXCFNKTFSLGDNFLDPNPLKIISVRRLNNFSQTNPNESDVDCQTGDESNCKTIPLNNYLCYDESISGFEEESVSECEFDSCFDSGIIDKNDFKSPNMSLTYELPIVNRFQILPDKTVREFPSIDEVNRYCINEKLKRLQAADKIQDPTQNIIPRKISQETQYDANQTCQIASKRSKEVPLDQSTLSPEILSNLPIDLLTDFINGEKSEKEVLNEIXXXXXXXXXXXXXXXXXXIDSVKNNLSQKLTKTTPSTKLAINSIKSQKNLSPKNHTIITDLSYCSLSNNQQIISKEAIIAHKLSEVDNNSILSDENALGKEIMSTQSNVNDSTSYSVKQNVLIEEPSFDSIDNYQTDFHATQTKDEKQNFDNNFLRNCSLQNFGYLKHEKILIGPNENSTGNTXXXXXXXXXXXXXXDGSKDTRTSSTDSGFHEIEPYYSNDKDQQEKSKNEIKTNEKIDPTEFIEIVHQTVTEGTTTQPNPNLHVQKPVDEPSSSQCSVSKHLDLSSFKFRFINESDLNKQNNKSIYNAVDLSSIDTHRKPDRYRNYNDSNQGKPRHNIINPSQTNLKYKSQSEIAQLSYSESHSNAXXXXXXXXXXXXXXXXXXXXXXGLLDKINQSNLTTTNTHDIVIYTQYCDPISSIEKYNPFRVNYYSPDYVISNKKEISLFLYFQWLKFCEQCTIENHNL 2217
            MVCKINFDYEILLSDNNDSITSSEISSDDECFNKTFSLGDNFLDPNPLKIISVRRLNNFSQTNPNESDVDCQTGDESNCKTIPLNNYLCYDESISGFEEESVSECEFDSCFDSGIIDKNDFKSPNMSLTYELPIVNRFQILPDKTVREFPSIDEVNRYCINEKLKRLQAADKIQDPTQNIIPRKISQETQYDANQTCQIASKRSKEVPLDQSTLSPEILSNLPIDLLTDFINGEKSEKEVLNEISKKSFKKRKKGKKSKRHKIDSVKNNLSQKLTKTTPSTKLAINSIKSQKNLSPKNHTIITDLSYCSLSNNQQIISKEAIIAHKLSEVDNNSILSDENALGKEIMSTQSNVNDSTSYSVKQNVLIEEPSFDSIDNYQTDFHATQTKDEKQNFDNNFLRNCSLQNFGYLKHEKILIGPNENSTGNTINNEIPISEISSIPDGSKDTRTSSTDSGFHEIEPYYSNDKDQQEKSKNEIKTNEKIDPTEFIEIVHQTVTEGTTTQPNPNLHVQKPVDEPSSSQCSVSKHLDLSSFKFRFINESDLNKQNNKSIYNAVDLSSIDTHRKPDRYRNYNDSNQGKPRHNIINPSQTNLKYKSQSEIAQLSYSESHSNADNYHHTHTDNHNQQQQHQQQNYGLLDKINQSNLTTTNTHDIVIYTQYCDPISSIEKYNPFRVNYYSPDYVISNKKEISLFLYFQWLKFCEQCTIENHNL
Sbjct:    1 MVCKINFDYEILLSDNNDSITSSEISSDDECFNKTFSLGDNFLDPNPLKIISVRRLNNFSQTNPNESDVDCQTGDESNCKTIPLNNYLCYDESISGFEEESVSECEFDSCFDSGIIDKNDFKSPNMSLTYELPIVNRFQILPDKTVREFPSIDEVNRYCINEKLKRLQAADKIQDPTQNIIPRKISQETQYDANQTCQIASKRSKEVPLDQSTLSPEILSNLPIDLLTDFINGEKSEKEVLNEISKKSFKKRKKGKKSKRHKIDSVKNNLSQKLTKTTPSTKLAINSIKSQKNLSPKNHTIITDLSYCSLSNNQQIISKEAIIAHKLSEVDNNSILSDENALGKEIMSTQSNVNDSTSYSVKQNVLIEEPSFDSIDNYQTDFHATQTKDEKQNFDNNFLRNCSLQNFGYLKHEKILIGPNENSTGNTINNEIPISEISSIPDGSKDTRTSSTDSGFHEIEPYYSNDKDQQEKSKNEIKTNEKIDPTEFIEIVHQTVTEGTTTQPNPNLHVQKPVDEPSSSQCSVSKHLDLSSFKFRFINESDLNKQNNKSIYNAVDLSSIDTHRKPDRYRNYNDSNQGKPRHNIINPSQTNLKYKSQSEIAQLSYSESHSNADNYHHTHTDNHNQQQQHQQQNYGLLDKINQSNLTTTNTHDIVIYTQYCDPISSIEKYNPFRVNYYSPDYVISNKKEISLFLYFQWLKFCEQCTIENHNL 711          
The following BLAST results are available for this feature:
BLAST of SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 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 SMED30023748 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000022731.10.000e+0100.00SMESG000022731.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023748 ID=SMED30023748|Name=SMED30023748|organism=Schmidtea mediterranea sexual|type=transcript|length=2347bp
GTAACAGAAAAGGAATTTTATATAAAATGAGAATTTGAATTTTTTAATTA
TAGAAAGACAAATTTTGATCTTATTCAAATCAAAATGGTTTGCAAGATAA
ATTTCGATTATGAAATTTTATTATCCGATAATAATGACTCAATTACTTCA
TCTGAAATATCCAGTGATGATGAGTGTTTCAATAAAACATTTTCACTTGG
AGACAATTTTCTAGACCCAAATCCTTTGAAAATCATTTCAGTGAGGCGAT
TGAATAATTTTTCACAAACTAACCCAAATGAATCAGACGTTGATTGTCAA
ACAGGTGATGAAAGCAATTGTAAAACGATTCCGTTGAATAATTATCTCTG
TTATGATGAATCGATAAGCGGTTTTGAAGAAGAATCTGTATCCGAGTGTG
AATTCGATTCATGTTTTGATTCGGGGATTATTGATAAAAATGATTTTAAG
AGTCCAAATATGTCATTAACTTACGAATTGCCAATAGTAAATAGATTTCA
AATACTCCCTGATAAAACTGTACGAGAATTTCCAAGTATTGATGAAGTTA
ATCGATATTGCATTAATGAAAAATTGAAACGATTGCAAGCAGCTGATAAA
ATTCAAGACCCAACTCAAAATATAATTCCAAGAAAAATCAGCCAAGAGAC
ACAATATGATGCCAATCAAACCTGTCAAATCGCATCGAAAAGATCGAAAG
AAGTGCCATTAGATCAATCTACATTATCCCCTGAAATATTATCCAACCTC
CCAATAGATTTATTAACCGATTTTATCAATGGAGAAAAATCGGAAAAAGA
AGTTTTGAATGAAATCAGCAAAAAATCTTTTAAAAAACGTAAAAAAGGCA
AAAAATCCAAACGGCATAAAATCGATTCTGTGAAAAATAATTTATCTCAG
AAACTGACCAAAACCACCCCATCGACCAAATTAGCAATTAATAGTATAAA
ATCTCAGAAAAATCTCTCGCCTAAAAACCACACAATAATTACCGATCTGT
CATATTGCTCCCTTTCCAATAATCAACAGATAATATCCAAAGAAGCCATA
ATTGCTCACAAATTATCAGAGGTTGATAACAATAGCATTCTTTCGGATGA
AAATGCCCTGGGAAAAGAAATTATGTCCACCCAATCAAATGTTAACGACT
CCACGTCTTATTCGGTTAAACAAAATGTTTTAATAGAAGAACCTTCATTC
GATTCTATCGACAACTACCAAACCGATTTCCACGCCACTCAAACAAAAGA
CGAGAAACAAAATTTTGATAATAATTTTCTCAGAAATTGTTCACTTCAAA
ATTTCGGTTACTTAAAACACGAGAAAATTCTGATTGGTCCAAATGAAAAT
TCTACCGGAAATACAATAAATAACGAAATCCCAATCTCAGAAATCTCATC
AATCCCCGATGGATCTAAGGACACAAGAACATCGAGCACTGACAGCGGAT
TTCATGAAATCGAACCTTACTATTCGAATGATAAAGATCAACAGGAAAAG
TCCAAAAATGAAATAAAAACCAACGAGAAAATCGATCCGACTGAATTTAT
CGAAATTGTGCACCAAACAGTCACAGAAGGAACAACAACCCAACCAAATC
CAAATTTACATGTGCAAAAACCAGTCGATGAACCATCTAGTTCCCAATGT
TCAGTTTCCAAGCATTTAGATTTATCTTCATTCAAATTCCGGTTCATCAA
TGAATCGGATTTAAACAAACAAAATAATAAATCCATTTACAACGCCGTCG
ACTTATCATCAATCGATACCCACAGAAAACCAGATCGCTACCGCAATTAT
AATGATAGCAATCAGGGTAAACCTCGCCACAATATAATAAATCCTTCACA
AACTAATCTCAAATACAAATCTCAATCAGAAATCGCACAATTATCGTATT
CAGAATCACATTCTAATGCCGACAATTATCATCATACTCATACTGATAAT
CATAATCAGCAGCAGCAACACCAGCAGCAAAATTATGGATTATTAGACAA
AATTAACCAATCAAATTTGACGACAACAAACACACACGATATTGTTATAT
ACACACAATATTGTGATCCAATCAGTTCCATTGAAAAATATAATCCATTC
AGAGTTAATTATTATTCGCCTGATTATGTCATCTCAAATAAAAAAGAAAT
TTCTCTATTTCTCTATTTTCAGTGGTTAAAGTTTTGTGAACAATGCACAA
TAGAAAACCATAATCTCTAAATCCTGTGAATAAAACTGTACAATTGGATA
AAATTTCCATTACAATGGTTGGATTTTAATTGAATTCAATTAATAACATT
GTTGAATTTTGTGCTTTTTATATTTAATAATTAATATTTACTCTCTC
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protein sequence of SMED30023748-orf-1

>SMED30023748-orf-1 ID=SMED30023748-orf-1|Name=SMED30023748-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=712bp
MVCKINFDYEILLSDNNDSITSSEISSDDECFNKTFSLGDNFLDPNPLKI
ISVRRLNNFSQTNPNESDVDCQTGDESNCKTIPLNNYLCYDESISGFEEE
SVSECEFDSCFDSGIIDKNDFKSPNMSLTYELPIVNRFQILPDKTVREFP
SIDEVNRYCINEKLKRLQAADKIQDPTQNIIPRKISQETQYDANQTCQIA
SKRSKEVPLDQSTLSPEILSNLPIDLLTDFINGEKSEKEVLNEISKKSFK
KRKKGKKSKRHKIDSVKNNLSQKLTKTTPSTKLAINSIKSQKNLSPKNHT
IITDLSYCSLSNNQQIISKEAIIAHKLSEVDNNSILSDENALGKEIMSTQ
SNVNDSTSYSVKQNVLIEEPSFDSIDNYQTDFHATQTKDEKQNFDNNFLR
NCSLQNFGYLKHEKILIGPNENSTGNTINNEIPISEISSIPDGSKDTRTS
STDSGFHEIEPYYSNDKDQQEKSKNEIKTNEKIDPTEFIEIVHQTVTEGT
TTQPNPNLHVQKPVDEPSSSQCSVSKHLDLSSFKFRFINESDLNKQNNKS
IYNAVDLSSIDTHRKPDRYRNYNDSNQGKPRHNIINPSQTNLKYKSQSEI
AQLSYSESHSNADNYHHTHTDNHNQQQQHQQQNYGLLDKINQSNLTTTNT
HDIVIYTQYCDPISSIEKYNPFRVNYYSPDYVISNKKEISLFLYFQWLKF
CEQCTIENHNL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 248..263
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 427..458
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 427..481
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 248..270
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 460..481