SMED30010847

Overview
NameSMED30010847
Smed IDSMED30010847
Length (bp)1447
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 SMED30010847 (SMED30010847) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010847 (SMED30010847) 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 SMED30010847 (SMED30010847) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010847 (SMED30010847) 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




SMED30010847

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30010847h1SMcG0019082 SmedASXL_009109SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30010847h1SMcG0019082 dd_Smed_v4_10187_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30010847h1SMcG0019082 dd_Smed_v4_10187_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30010847h1SMcG0019082 dd_Smed_v4_10187_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30010847h1SMcG0019082 dd_Smed_v4_10187_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30010847h1SMcG0019082 dd_Smed_v4_10187_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30010847h1SMcG0019082 dd_Smed_v6_10187_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30010847h1SMcG0019082 OX_Smed_1.0.15906ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30010847 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000000:77523..78969 -7208
Homology
BLAST of SMED30010847 vs. Planmine SMEST
Match: SMESG000026789.1 (SMESG000026789.1)

HSP 1 Score: 729.939 bits (1883), Expect = 0.000e+0
Identity = 414/414 (100.00%), Postives = 414/414 (100.00%), Query Frame = 2
Query:  179 MIMNNHIFFMTIKDRIYCLTSSSILLPMSIFIGVTTFQNLDQNNQILEIYILIVRCAFSITGTIAGLLCTFVVVACPKRNXXXXXXXXXXXXXFGALITIATTIFSTDWADQRQSLTKTIFILTSILAFVSAVTICICLLNRFKKSDFRYDDPTECVEHASCILAALFIISAFTSIIGFTMGYTVSQQLVGVRILGGGSHSGIFGLLSTTLFILAICINXXXXXXXXXXXXXXXXXXXXXXXVSYYTEEMEYTQSLKYIEKNSILFYKSINLKLMLLTKHTLVLVTSVFNLVFAAPLTVXXXXXXXXXXXXXXRVNEEPNQPQHELNYTYQFSQLRTPLLHNCMQYSNIESSPTLPMNSNSRQKLISQVNIVENNAINFVNSNHQMRPVEPKTSNMNSNVQTCDLLKPLWQSSG 1420
            MIMNNHIFFMTIKDRIYCLTSSSILLPMSIFIGVTTFQNLDQNNQILEIYILIVRCAFSITGTIAGLLCTFVVVACPKRNLSLITLLISILSTFGALITIATTIFSTDWADQRQSLTKTIFILTSILAFVSAVTICICLLNRFKKSDFRYDDPTECVEHASCILAALFIISAFTSIIGFTMGYTVSQQLVGVRILGGGSHSGIFGLLSTTLFILAICINKKLKLIFLSISLGLGILALVASSVSYYTEEMEYTQSLKYIEKNSILFYKSINLKLMLLTKHTLVLVTSVFNLVFAAPLTVLICCLLKDDLLITTRVNEEPNQPQHELNYTYQFSQLRTPLLHNCMQYSNIESSPTLPMNSNSRQKLISQVNIVENNAINFVNSNHQMRPVEPKTSNMNSNVQTCDLLKPLWQSSG
Sbjct:    1 MIMNNHIFFMTIKDRIYCLTSSSILLPMSIFIGVTTFQNLDQNNQILEIYILIVRCAFSITGTIAGLLCTFVVVACPKRNLSLITLLISILSTFGALITIATTIFSTDWADQRQSLTKTIFILTSILAFVSAVTICICLLNRFKKSDFRYDDPTECVEHASCILAALFIISAFTSIIGFTMGYTVSQQLVGVRILGGGSHSGIFGLLSTTLFILAICINKKLKLIFLSISLGLGILALVASSVSYYTEEMEYTQSLKYIEKNSILFYKSINLKLMLLTKHTLVLVTSVFNLVFAAPLTVLICCLLKDDLLITTRVNEEPNQPQHELNYTYQFSQLRTPLLHNCMQYSNIESSPTLPMNSNSRQKLISQVNIVENNAINFVNSNHQMRPVEPKTSNMNSNVQTCDLLKPLWQSSG 414          
BLAST of SMED30010847 vs. Planmine SMEST
Match: SMESG000030973.1 (SMESG000030973.1)

HSP 1 Score: 207.608 bits (527), Expect = 7.907e-62
Identity = 165/412 (40.05%), Postives = 253/412 (61.41%), Query Frame = 2
Query:  191 NHIFFMTIKDRIYCLTSSSILLPMSIFIGVTTFQNLDQNNQILEIYILIVRCAFSITGTIAGLLCTFVVVACPKRNXXXXXXXXXXXXXFGALITIATTIFSTDWADQRQSLTKTIFILTSILAFVSAVTICICLLNRFKKSDFRYDD-PTECVEHASCILAALFIISAFTSIIGFTMGYTVSQQLVGVRILGGGSHSGIFGLLSTTLFILAICINXXXXXXXXXXXXXXXXXXXXXXXVSYYTEEMEYTQSLKYIEKNSILF-----YKSINLKLMLLTKHTLVLVTSVFNLVFAAPLTVXXXXXXXXXXXXXXRVNEEPNQPQHELNYTYQFSQLRTPLLHNCMQYSNIESSPTLPMNSNS-RQKLISQVNIVENNAINFVNSNHQMRPVEPKTSNMNSNVQTCDLLKPL 1405
            N+ FF+TI DR+ CL S++ILLPMS+FI   T + L   +   ++YI+ ++   SI+G +  +L  FV +ACP R +S+  +++S +S FG ++++AT  F  +W    ++++K +FI+TS L  V +V I + +  RFK S F +D   T  +E  S ILA L II++FTSI GF MGY +  QL+  RI GGG HSGI GLLS+ +F+ AI    K +   LSIS+G+ ILAL++ ++SYYTEE+E   S+++I K+ +LF     Y+    K++L+TK TL+L++S+F LVF  PLTV  CCLLK DLLI   +    N+   ++++    S  + P L+N   +  +ES  TL  NS + +   +S +N V     N V S + +R  +P +S  ++    CDLLK +
Sbjct:    6 NNRFFLTIHDRVCCLLSAAILLPMSLFIIAVTIRQLSTISSTEDVYIVSIKSLSSISGILTAILSIFVSIACPYRRISITNIVLSTISAFGIMMSLATIFFHANWNGHHEAVSKVVFIITSSLCLVCSVVITMRIALRFK-SQFVFDSIQTTFLEQCSIILATLLIIASFTSISGFVMGYIIKWQLLIDRIFGGGLHSGIMGLLSSLVFLAAIYGGPKSRFSLLSISMGVSILALISLAISYYTEEIEIDHSIQFISKHQLLFIVPNYYR----KVLLMTKSTLILISSIFGLVFGTPLTVATCCLLKRDLLIQPELMNIRNEC--DIDFMCSPSINQDPFLYNAPPH--VESMKTLYNNSFTLKPHFMSTLNSVYCPP-NTVESINMLRS-QPMSSPNSTKEDVCDLLKEI 406          
BLAST of SMED30010847 vs. Planmine SMEST
Match: SMESG000050120.1 (SMESG000050120.1)

HSP 1 Score: 115.931 bits (289), Expect = 2.626e-28
Identity = 97/305 (31.80%), Postives = 181/305 (59.34%), Query Frame = 2
Query:  179 MIMNNHIFFMTIKDRIYCLTSSSILLPMSIFIGVTTFQ--NLDQNNQILEIYILIVRCAFSITGTIAGLLCTFVVVACPKRNXXXXXXXXXXXXXFGALITIATTIFSTDWADQRQSLTKTIFILTSILAFVSAVTICICLLNRFKKSDF--RYDDPTECVEHASCILAALFIISAFTSIIGFTMGYTVSQQLVGVR-ILGGGSHSGIFGLLSTTLFILAICI-NXXXXXXXXXXXXXXXXXXXXXXXVSYYTEEMEYTQSLKYIEKNSILFYKSINLKLMLLTKHTLVLVTSVFNLVFAAPLTV 1075
            M++ + + F++    I CL +SSIL+P SIF+  +T +  +LDQ   ++ +Y+L V+ A S  G    LL     V  PK+ +  I +++ ILS+FGA+++I+T  F ++W    +++   +F++  I+  ++A+ + I +  RFK  D    Y +    +  +  +++AL ++++ TS IGF +G  V+ QL+    ++GGG +SG  G+L   L++  + +   K +L+   I + LG+L  V +  S++TEE+E   +++YI+ N +L  + I+ K++LL K TLV+++S+F  VF  P+ V
Sbjct:    1 MVIFSSMSFLSPVGSIICLYTSSILMPASIFVLSSTVRQVSLDQLRDVMTLYVLGVKVATSFLGISTSLLAHVTAVFWPKKLICWILMIMGILSSFGAMMSISTIFFKSNWNSHIEAMRHIMFLVAEIVIMITAMVLSIKIALRFKSPDEYENYYNGESFIIISGVLISALLLLASITSFIGFIIGIYVNTQLLRESTVVGGGLYSGFLGILIGILYLSGVKLCKLKAQLVMHPIIIMLGVLDFVGAITSFFTEELELAATIEYIKNNQLLSNEYIHYKILLLCKSTLVMLSSLFMAVFICPMIV 305          
The following BLAST results are available for this feature:
BLAST of SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 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 SMED30010847 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000026789.10.000e+0100.00SMESG000026789.1[more]
SMESG000030973.17.907e-6240.05SMESG000030973.1[more]
SMESG000050120.12.626e-2831.80SMESG000050120.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010847 ID=SMED30010847|Name=SMED30010847|organism=Schmidtea mediterranea sexual|type=transcript|length=1447bp
GTGGAAATAGAATCGTTTTCCACTACGATACGACAAGAATTGAGATTTAT
TATTTCAGTGTTGAGGAGCTTCGTCTATGAATCAGAAATTCCGAAAACGA
TAACCGTTTCCATTGGCAACAGAGAGAAAGAGAGACAAAGAGATAGAAAG
AGAGTGAGCGAGAGACAAAAAGTTAACCATGATAATGAACAATCACATCT
TTTTCATGACGATAAAAGACAGAATTTATTGTCTGACAAGTTCTTCGATT
CTTTTACCTATGAGCATTTTCATTGGAGTGACGACCTTTCAAAATCTCGA
TCAAAACAATCAAATTCTCGAGATCTACATTTTGATCGTTCGATGTGCGT
TCTCAATAACCGGAACCATTGCTGGACTGCTGTGTACGTTTGTTGTCGTT
GCTTGCCCGAAACGCAATCTCTCATTGATCACGCTTTTGATTAGTATTTT
GTCGACATTCGGTGCTCTGATCACGATCGCAACGACGATCTTCAGTACAG
ATTGGGCGGATCAGCGACAGTCGTTGACGAAAACAATTTTCATTTTAACA
TCAATTCTTGCGTTTGTTTCCGCAGTGACGATTTGTATTTGTCTGTTGAA
CCGATTCAAAAAATCCGATTTCAGATACGATGATCCGACAGAATGCGTTG
AACACGCCAGCTGCATCCTTGCTGCGTTGTTTATCATTTCGGCATTCACG
TCTATTATTGGGTTTACTATGGGTTATACAGTTAGTCAACAATTGGTCGG
GGTCAGAATTCTTGGAGGGGGCTCTCATTCTGGGATATTTGGATTGTTAT
CAACCACTCTCTTTATTCTTGCAATTTGTATAAATAAGAAACTGAAATTA
ATTTTCCTTAGCATTTCCCTAGGACTCGGCATCCTAGCTCTAGTAGCGTC
ATCAGTTTCCTATTACACCGAAGAGATGGAATACACGCAATCGTTGAAAT
ATATAGAGAAAAATTCTATTCTTTTTTATAAAAGTATAAATCTCAAACTC
ATGCTGTTAACGAAACATACCTTAGTATTGGTGACATCAGTATTCAACCT
AGTATTTGCGGCTCCGTTAACCGTTTTGATTTGTTGTTTATTAAAGGATG
ATCTTTTGATAACGACTCGAGTAAACGAAGAACCGAATCAACCTCAACAC
GAGTTAAATTATACGTATCAGTTTTCACAACTCCGCACACCTTTGCTGCA
CAATTGCATGCAATACTCCAATATAGAATCGAGTCCAACTCTACCGATGA
ATTCAAATTCGAGACAGAAACTTATCTCCCAGGTGAACATCGTGGAGAAT
AATGCTATAAACTTTGTCAACTCCAACCATCAAATGAGACCAGTCGAGCC
AAAGACAAGCAACATGAATAGCAACGTACAAACTTGTGACCTACTCAAGC
CATTATGGCAAAGTAGTGGATAATATTATCATAATAATATCTTGTAC
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protein sequence of SMED30010847-orf-1

>SMED30010847-orf-1 ID=SMED30010847-orf-1|Name=SMED30010847-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=415bp
MIMNNHIFFMTIKDRIYCLTSSSILLPMSIFIGVTTFQNLDQNNQILEIY
ILIVRCAFSITGTIAGLLCTFVVVACPKRNLSLITLLISILSTFGALITI
ATTIFSTDWADQRQSLTKTIFILTSILAFVSAVTICICLLNRFKKSDFRY
DDPTECVEHASCILAALFIISAFTSIIGFTMGYTVSQQLVGVRILGGGSH
SGIFGLLSTTLFILAICINKKLKLIFLSISLGLGILALVASSVSYYTEEM
EYTQSLKYIEKNSILFYKSINLKLMLLTKHTLVLVTSVFNLVFAAPLTVL
ICCLLKDDLLITTRVNEEPNQPQHELNYTYQFSQLRTPLLHNCMQYSNIE
SSPTLPMNSNSRQKLISQVNIVENNAINFVNSNHQMRPVEPKTSNMNSNV
QTCDLLKPLWQSSG*
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protein sequence of SMED30010847-orf-2

>SMED30010847-orf-2 ID=SMED30010847-orf-2|Name=SMED30010847-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=148bp
VEIESFSTTIRQELRFIISVLRSFVYESEIPKTITVSIGNREKERQRDRK
RVSERQKVNHDNEQSHLFHDDKRQNLLSDKFFDSFTYEHFHWSDDLSKSR
SKQSNSRDLHFDRSMCVLNNRNHCWTAVYVCCRCLPETQSLIDHAFD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 53..75
NoneNo IPR availableTMHMMTMhelixcoord: 199..218
NoneNo IPR availableTMHMMTMhelixcoord: 162..184
NoneNo IPR availableTMHMMTMhelixcoord: 283..305
NoneNo IPR availableTMHMMTMhelixcoord: 82..104
NoneNo IPR availableTMHMMTMhelixcoord: 225..247
NoneNo IPR availableTMHMMTMhelixcoord: 16..38
NoneNo IPR availableTMHMMTMhelixcoord: 119..141