SMED30002886

Overview
NameSMED30002886
Smed IDSMED30002886
Length (bp)820
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 SMED30002886 (SMED30002886) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002886 (SMED30002886) 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 SMED30002886 (SMED30002886) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002886 (SMED30002886) 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



SMED30002886

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 regionSMED30002886SMESG000017779.1 SmedASXL_009536SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30002886SMESG000017779.1 dd_Smed_v4_11049_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30002886SMESG000017779.1 dd_Smed_v4_11049_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30002886SMESG000017779.1 dd_Smed_v4_11049_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30002886SMESG000017779.1 dd_Smed_v6_11049_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30002886SMESG000017779.1 dd_Smed_v4_11049_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30002886SMESG000017779.1 dd_Smed_v4_11049_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
whole organismSMED30002886SMESG000017779.1 dd_Smed_v4_11049_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002886 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002502:27258..35930 -3995
Homology
[Close]
BLAST of SMED30002886 vs. TrEMBL
Match: A0A267EXH3 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig019845g1 PE=4 SV=1)

HSP 1 Score: 126.331 bits (316), Expect = 2.469e-31
Identity = 88/253 (34.78%), Postives = 118/253 (46.64%), Query Frame = 2 
Query:   26 MASNVELSIEPVAPLIVDPNYDIHTQRPRTPNIPYSNYSETQIKNIHQNEETFFHYL-------PVLPD------FDYNKYKKKLVDFD------------YTSDEASCRSRARHNASRPGAYFHWGKFPSPGDNICKHFHCESKESFTEIDMYRRPPTNRPGRIVMKFGRPNRDYYAPKYPSSTTWFQSDCPLNQCASFGMNKPMTFKQHNAYKKEEKDYFKSQM--SKYPNISEYIDKYTLENRTMPTMTN 703
            MASNVEL          D + D +T  P+TPN+PYSN +  Q K+I +N   FFH           +PD      +  ++Y   +                Y  D         H+ASRPGAYF WG   + G+    HF  ES  +F  +D Y RPPTN PG I  K+GRP   YYA + P S TWF S   LN+       +P T  ++     E +    ++    KYP  SEY  KYT++ RT PT ++
Sbjct:    1 MASNVELKRTKNLEYSCDESTDPYTGLPKTPNVPYSNMTSEQEKSIKKNPHAFFHESKEEPREPGCIPDPREGGRYYIDRYADSMSQHLFRDQPTPSNPHCYIGDRLDRELPPDHSASRPGAYFSWGPNRA-GEKTLGHFDGESPVAFLPVDTYHRPPTNLPGEITFKYGRPGDGYYAQRNPQSNTWFASSHRLNEQRILQNIRPKTLAEYEQISSESRSLAATRRDEEKYPEYSEYTAKYTVQERT-PTASS 251
[Close]
BLAST of SMED30002886 vs. TrEMBL
Match: A0A267FGG0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig003160g1 PE=4 SV=1)

HSP 1 Score: 126.331 bits (316), Expect = 2.576e-31
Identity = 88/253 (34.78%), Postives = 118/253 (46.64%), Query Frame = 2 
Query:   26 MASNVELSIEPVAPLIVDPNYDIHTQRPRTPNIPYSNYSETQIKNIHQNEETFFHYL-------PVLPD------FDYNKYKKKLVDFD------------YTSDEASCRSRARHNASRPGAYFHWGKFPSPGDNICKHFHCESKESFTEIDMYRRPPTNRPGRIVMKFGRPNRDYYAPKYPSSTTWFQSDCPLNQCASFGMNKPMTFKQHNAYKKEEKDYFKSQM--SKYPNISEYIDKYTLENRTMPTMTN 703
            MASNVEL          D + D +T  P+TPN+PYSN +  Q K+I +N   FFH           +PD      +  ++Y   +                Y  D         H+ASRPGAYF WG   + G+    HF  ES  +F  +D Y RPPTN PG I  K+GRP   YYA + P S TWF S   LN+       +P T  ++     E +    ++    KYP  SEY  KYT++ RT PT ++
Sbjct:    1 MASNVELKRTKNLEYSCDESTDPYTGLPKTPNVPYSNMTSEQEKSIKKNPHAFFHESKEEPREPGCIPDPREGGRYYIDRYANSMSQHLFRDQPTPSNPHCYIGDRLDRELPPDHSASRPGAYFSWGPNRA-GEKTLGHFDGESPVAFLPVDTYHRPPTNLPGEITFKYGRPGDGYYAQRNPQSNTWFASSHRLNEQRILQNIRPKTLAEYEQISSESRSLAATRRDEEKYPEYSEYTAKYTVQERT-PTASS 251
[Close]
BLAST of SMED30002886 vs. TrEMBL
Match: A0A1I8IGQ4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 116.701 bits (291), Expect = 1.192e-27
Identity = 83/244 (34.02%), Postives = 115/244 (47.13%), Query Frame = 2 
Query:   26 MASNVELSIEPVAPLIVDPNYDIHTQRPRTPNIPYSNYSET-QIKNIHQNEETFFHYLPVLPD---FDYNKYKKKLVDFD------------YTSDEASCRSRARHNASRPGAYFHWGKFPSPGDNICKHFHCESKESFTEIDMYRRPPTNRPGRIVMKFGRPNRDYYAPKYPSSTTWFQSDCPLNQCASFGMNKPMTFKQHNAYKKEEKDYFKSQM--SKYPNISEYIDKYTLENRTMPTMTN 703
            MASNVEL          D + D +T  P+TPN+PYSN +++ +I +  Q         P  P+   +  ++Y   +                Y  D         H+ASRPGAYF WG   + G+    HF  ES  +F  +D Y RPPTN PG I  K+GRP   YYA + P S TWF S   LN+       +P T  ++     E +    ++    KYP  SEY  KYT++ RT PT ++
Sbjct:    1 MASNVELKRTKNLEYSCDESTDPYTGLPKTPNVPYSNMTKSARIFSRVQGGAARARLHPGSPEGGRYYIDRYADSMSQHLFRDQPTPSNPHCYIGDRLDRELPPDHSASRPGAYFSWGPNRA-GEKTLGHFDGESPVAFLPVDTYHRPPTNLPGEITFKYGRPGDGYYAQRNPQSNTWFASSHRLNEQRILQNIRPKTLAEYEQISSESRSLAATRRDEEKYPEYSEYTAKYTVQERT-PTASS 242
[Close]
BLAST of SMED30002886 vs. TrEMBL
Match: A0A1I8HDV6 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 116.316 bits (290), Expect = 1.230e-27
Identity = 83/244 (34.02%), Postives = 115/244 (47.13%), Query Frame = 2 
Query:   26 MASNVELSIEPVAPLIVDPNYDIHTQRPRTPNIPYSNYSET-QIKNIHQNEETFFHYLPVLPD---FDYNKYKKKLVDFD------------YTSDEASCRSRARHNASRPGAYFHWGKFPSPGDNICKHFHCESKESFTEIDMYRRPPTNRPGRIVMKFGRPNRDYYAPKYPSSTTWFQSDCPLNQCASFGMNKPMTFKQHNAYKKEEKDYFKSQM--SKYPNISEYIDKYTLENRTMPTMTN 703
            MASNVEL          D + D +T  P+TPN+PYSN +++ +I +  Q         P  P+   +  ++Y   +                Y  D         H+ASRPGAYF WG   + G+    HF  ES  +F  +D Y RPPTN PG I  K+GRP   YYA + P S TWF S   LN+       +P T  ++     E +    ++    KYP  SEY  KYT++ RT PT ++
Sbjct:    1 MASNVELKRTKNLEYSCDESTDPYTGLPKTPNVPYSNMTKSARIFSRVQGGAARARLHPGSPEGGRYYIDRYADSMSQHLFRDQPTPSNPHCYIGDRLDRELPPDHSASRPGAYFSWGPNRA-GEKTLGHFDGESPVAFLPVDTYHRPPTNLPGEITFKYGRPGDGYYAQRNPQSNTWFASSHRLNEQRILQNIRPKTLAEYEQISSESRSLAATRRDEEKYPEYSEYTAKYTVQERT-PTASS 242
[Close]
BLAST of SMED30002886 vs. TrEMBL
Match: A0A2T7PUJ2 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_04085 PE=4 SV=1)

HSP 1 Score: 112.464 bits (280), Expect = 3.474e-26
Identity = 76/236 (32.20%), Postives = 108/236 (45.76%), Query Frame = 2 
Query:   71 IVDPNYDIHTQRPRTPNIPYSNYSETQIKN--IHQNEETFFHYLPVL----PDFDYNKYKKKLVDFD-----------YTSDEASCRSRARHNASRPGAYFHWGKFPSPGDNICKHFHCESKESFTEIDMYRRPPTNRPGRIVMKFGRPNRDYYAPKYPSSTTWFQSDCPLNQCASFGMNKPMTFKQHNAYKKEEKDYFKSQMSKYPNISEYIDKYTLENRTMPTMTNMERRIAHL 727
            +   N D+ T+RPRTP+  Y+  +E QI N  I+     FF     L      +  ++Y      +            +  D    +   +HN  R GA   WG   + G     HF  E    +  ID+Y RPPTN  G +V K GRP R YY  ++P S TWF S   LNQ       +P T K+H    + EK     +  K+P  SEY+D+YTL ++  P +T+ ER   H+
Sbjct:    1 MASENIDMITKRPRTPHDQYTCMTEEQIHNNTINGRPNRFFMSQKPLVMSKKRYCMDRYATNTSQYLFREQPRSYPKCWIGDLWQQQPSEQHNTCRLGASLRWGPEKN-GSRTYSHFVGEDTHRYLNIDVYCRPPTNLVGLVVQKHGRPGRSYYDQRHPHSATWFGSSHILNQTDILQDIRPKTLKEHQMSSEAEKTKMIWRHGKWPEFSEYVDRYTLHSKDEPELTSFERNKRHI 235
[Close]
BLAST of SMED30002886 vs. Planmine SMEST
Match: SMESG000017779.1 (SMESG000017779.1)

HSP 1 Score: 499.975 bits (1286), Expect = 0.000e+0
Identity = 237/238 (99.58%), Postives = 237/238 (99.58%), Query Frame = 2 
Query:   26 MASNVELSIEPVAPLIVDPNYDIHTQRPRTPNIPYSNYSETQIKNIHQNEETFFHYLPVLPDFDYNKYKKKLVDFDYTSDEASCRSRARHNASRPGAYFHWGKFPSPGDNICKHFHCESKESFTEIDMYRRPPTNRPGRIVMKFGRPNRDYYAPKYPSSTTWFQSDCPLNQCASFGMNKPMTFKQHNAYKKEEKDYFKSQMSKYPNISEYIDKYTLENRTMPTMTNMERRIAHLRGTL 739
            MASNVELSIEPVAPLIVDPNYDIHTQRPRTPNIPYSNYSETQIKNIHQNEETFFHYLPVLPDFDYNKYKKKLVDFDYTSDEASCRSRARHNASRPGAYFHWG FPSPGDNICKHFHCESKESFTEIDMYRRPPTNRPGRIVMKFGRPNRDYYAPKYPSSTTWFQSDCPLNQCASFGMNKPMTFKQHNAYKKEEKDYFKSQMSKYPNISEYIDKYTLENRTMPTMTNMERRIAHLRGTL
Sbjct:    1 MASNVELSIEPVAPLIVDPNYDIHTQRPRTPNIPYSNYSETQIKNIHQNEETFFHYLPVLPDFDYNKYKKKLVDFDYTSDEASCRSRARHNASRPGAYFHWGTFPSPGDNICKHFHCESKESFTEIDMYRRPPTNRPGRIVMKFGRPNRDYYAPKYPSSTTWFQSDCPLNQCASFGMNKPMTFKQHNAYKKEEKDYFKSQMSKYPNISEYIDKYTLENRTMPTMTNMERRIAHLRGTL 238
The following BLAST results are available for this feature:
BLAST of SMED30002886 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 SMED30002886 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 SMED30002886 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 SMED30002886 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 SMED30002886 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 SMED30002886 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 SMED30002886 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 SMED30002886 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267EXH32.469e-3134.78Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FGG02.576e-3134.78Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8IGQ41.192e-2734.02Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8HDV61.230e-2734.02Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A2T7PUJ23.474e-2632.20Uncharacterized protein OS=Pomacea canaliculata OX... [more]
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BLAST of SMED30002886 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 SMED30002886 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 SMED30002886 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 SMED30002886 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 SMED30002886 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 SMED30002886 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000017779.10.000e+099.58SMESG000017779.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002886 ID=SMED30002886|Name=SMED30002886|organism=Schmidtea mediterranea sexual|type=transcript|length=820bp
CTTAAATAAATTTATTTAATTTTCAATGGCAAGCAATGTTGAATTATCGA
TTGAACCAGTTGCTCCATTAATTGTTGATCCAAATTATGATATTCACACT
CAAAGACCAAGAACTCCTAATATACCTTATTCCAATTATAGTGAAACACA
AATAAAAAATATACACCAAAACGAAGAAACATTCTTTCATTATCTACCAG
TACTTCCGGATTTCGATTACAATAAATATAAGAAAAAATTAGTTGACTTT
GACTATACATCTGACGAAGCCAGCTGTCGTTCAAGAGCTCGTCACAATGC
TTCAAGACCTGGTGCTTATTTTCATTGGGGAAAATTTCCATCTCCAGGAG
ATAATATCTGTAAACATTTTCATTGTGAGTCAAAAGAGAGTTTTACTGAA
ATCGACATGTACCGTCGACCACCAACAAACCGGCCTGGACGAATTGTTAT
GAAATTTGGAAGACCAAATCGTGATTATTATGCTCCGAAATATCCATCCT
CAACAACTTGGTTTCAATCTGATTGCCCATTGAACCAATGCGCGTCTTTC
GGAATGAATAAGCCAATGACATTCAAGCAGCACAATGCTTATAAAAAAGA
GGAGAAAGATTATTTTAAGTCACAAATGTCAAAATATCCCAATATATCTG
AATATATTGATAAATATACACTAGAAAATAGAACTATGCCGACAATGACA
AACATGGAAAGAAGAATCGCTCATCTCCGAGGCACACTTTAAGAATTCCT
TATGCAAATCCTTATTTTAACTGTAATAGAAATTATTTTTTGTATTGTAG
AATATAAATATAAAGTTTTG
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protein sequence of SMED30002886-orf-1

>SMED30002886-orf-1 ID=SMED30002886-orf-1|Name=SMED30002886-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=239bp
MASNVELSIEPVAPLIVDPNYDIHTQRPRTPNIPYSNYSETQIKNIHQNE
ETFFHYLPVLPDFDYNKYKKKLVDFDYTSDEASCRSRARHNASRPGAYFH
WGKFPSPGDNICKHFHCESKESFTEIDMYRRPPTNRPGRIVMKFGRPNRD
YYAPKYPSSTTWFQSDCPLNQCASFGMNKPMTFKQHNAYKKEEKDYFKSQ
MSKYPNISEYIDKYTLENRTMPTMTNMERRIAHLRGTL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000136whole organism
PLANA:0000418head