SMED30015561

Overview
NameSMED30015561
Smed IDSMED30015561
Length (bp)1318
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 SMED30015561 (SMED30015561) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015561 (SMED30015561) 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 SMED30015561 (SMED30015561) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015561 (SMED30015561) 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



SMED30015561

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30015561 SmedASXL_008940SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30015561 dd_Smed_v4_6429_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30015561 dd_Smed_v4_6429_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30015561 dd_Smed_v4_6429_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30015561 dd_Smed_v4_6429_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30015561 dd_Smed_v4_6429_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30015561 Contig45536newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30015561 Contig45536uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30015561 dd_Smed_v6_6429_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30015561 dd_Smed_v4_6429_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30015561 dd_Smed_v4_6429_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
SMED30015561 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002158:10682..33193 -5665
Homology
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BLAST of SMED30015561 vs. TrEMBL
Match: A0A267F9W5 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig000374g1 PE=4 SV=1)

HSP 1 Score: 100.523 bits (249), Expect = 6.479e-19
Identity = 70/189 (37.04%), Postives = 108/189 (57.14%), Query Frame = 3 
Query:  600 PKDPYQGPMVNLYFPFGSSGGGAPRRDNQGRIQTTFVGPEYLNVNIDEKKRKILASKAIXXXXXXXXXXXXXXXXXXXXXNREPNGDF-TELISSFKGGRPKRDPLTGMLINNHLQSSDVTNMKLASPRATSPWIPNEMVSMSNVDTL-TYGMELAKAAKERQVMKHLDKLRERQECKQHVDAWNNIWG 1160
            P   Y G   + YFPFG  G GAP  D++G +  +  G      ++ EK+RK LA++   +  QQEM++Q L R  +KQQ R P  DF TE ++    G+P RDP TG L++ HL SSD+T++   +PR     +       + VD   TYG +L +AA+ER  ++ L++L++ QE  QH + +  ++G
Sbjct:  354 PSHRYYGGSGDPYFPFGKPGSGAPIVDSKGNLVPSVYGAIEHEEHVSEKQRKALAARIYSQELQQEMIEQSLSRRLEKQQRRAPVDDFLTEQLARGAVGKPVRDPHTGYLLDQHLPSSDITHINYKTPRHKFQSVTGYQHLPAFVDDAGTYGTDLQRAAEERAALRQLERLQDVQEANQHANTFEGMFG 542
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BLAST of SMED30015561 vs. TrEMBL
Match: A0A1I8FTN0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 99.7525 bits (247), Expect = 1.111e-18
Identity = 70/189 (37.04%), Postives = 108/189 (57.14%), Query Frame = 3 
Query:  600 PKDPYQGPMVNLYFPFGSSGGGAPRRDNQGRIQTTFVGPEYLNVNIDEKKRKILASKAIXXXXXXXXXXXXXXXXXXXXXNREPNGDF-TELISSFKGGRPKRDPLTGMLINNHLQSSDVTNMKLASPRATSPWIPNEMVSMSNVDTL-TYGMELAKAAKERQVMKHLDKLRERQECKQHVDAWNNIWG 1160
            P   Y G   + YFPFG  G GAP  D++G +  +  G      ++ EK+RK LA++   +  QQEM++Q L R  +KQQ R P  DF TE ++    G+P RDP TG L++ HL SSD+T++   +PR     +       + VD   TYG +L +AA+ER  ++ L++L++ QE  QH + +  ++G
Sbjct:  403 PSHRYYGGSGDPYFPFGKPGSGAPIVDSKGNLVPSVYGAIEHEEHVSEKQRKALAARIYSQELQQEMIEQSLSRRLEKQQRRAPVDDFLTEQLARGAVGKPVRDPHTGYLLDQHLPSSDITHINYKTPRHKFQSVTGYQHLPAFVDDAGTYGTDLQRAAEERAALRQLERLQDVQEANQHANTFEGMFG 591
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BLAST of SMED30015561 vs. TrEMBL
Match: A0A267GWT6 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig000374g3 PE=4 SV=1)

HSP 1 Score: 99.7525 bits (247), Expect = 1.145e-18
Identity = 70/189 (37.04%), Postives = 108/189 (57.14%), Query Frame = 3 
Query:  600 PKDPYQGPMVNLYFPFGSSGGGAPRRDNQGRIQTTFVGPEYLNVNIDEKKRKILASKAIXXXXXXXXXXXXXXXXXXXXXNREPNGDF-TELISSFKGGRPKRDPLTGMLINNHLQSSDVTNMKLASPRATSPWIPNEMVSMSNVDTL-TYGMELAKAAKERQVMKHLDKLRERQECKQHVDAWNNIWG 1160
            P   Y G   + YFPFG  G GAP  D++G +  +  G      ++ EK+RK LA++   +  QQEM++Q L R  +KQQ R P  DF TE ++    G+P RDP TG L++ HL SSD+T++   +PR     +       + VD   TYG +L +AA+ER  ++ L++L++ QE  QH + +  ++G
Sbjct:  382 PSHRYYGGSGDPYFPFGKPGSGAPIVDSKGNLVPSVYGAIEHEEHVSEKQRKALAARIYSQELQQEMIEQSLSRRLEKQQRRAPVDDFLTEQLARGAVGKPVRDPHTGYLLDQHLPSSDITHINYKTPRHKFQSVTGYQHLPAFVDDAGTYGTDLQRAAEERAALRQLERLQDVQEANQHANTFEGMFG 570
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BLAST of SMED30015561 vs. TrEMBL
Match: A0A433T2W7 (Uncharacterized protein OS=Elysia chlorotica OX=188477 GN=EGW08_016351 PE=4 SV=1)

HSP 1 Score: 80.1073 bits (196), Expect = 2.155e-12
Identity = 54/176 (30.68%), Postives = 92/176 (52.27%), Query Frame = 3 
Query:  636 YFPFGSSGGGAPRRDNQGRIQTTFVGP-EYLNVNIDEKKRKILASKAIXXXXXXXXXXXXXXXXXXXXXNREPNGDFTELISSFKGGRPKRDPLTGMLINNHLQSSDVTNMKLASPRATSPWIPNEMVSMSNVDTLTYGMELAKAAKERQVMKHLDKLRERQECKQHVDAWNNIWG 1160
            Y+P+G  GGGAP RD +G+++T   G  E  N    + +R     + +    ++   QQ+  + +  +  + P  +  +++++ + G+P+RD +TG +  +HL +SDVT +K+          P  M    N     Y  EL K A+ERQ +K L+KL+ERQE   H    ++ WG
Sbjct:  258 YYPWGGQGGGAPIRDREGKVKTMIYGQLESKNNYSGDFRRAKRRQEVLYNELKEGERQQKQNKEELDRYMKAPQAELADVLAAGRVGKPRRDEITGEISQHHLPNSDVTLVKMNHQ-------PKPMDEKKN-----YHDELVKMAEERQHLKQLEKLKERQESNAHFRNMDSTWG 421
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BLAST of SMED30015561 vs. TrEMBL
Match: A0A2T7PR82 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_02894 PE=4 SV=1)

HSP 1 Score: 79.337 bits (194), Expect = 5.531e-12
Identity = 58/176 (32.95%), Postives = 78/176 (44.32%), Query Frame = 3 
Query:  633 LYFPFGSSGGGAPRRDNQGRIQTTFVGPEYLNVNIDEKKRKILASKAIXXXXXXXXXXXXXXXXXXXXXNREPNGDFTELISSFKGGRPKRDPLTGMLINNHLQSSDVTNMKLASPRATSPWIPNEMVSMSNVDTLTYGMELAKAAKERQVMKHLDKLRERQECKQHVDAWNNIWG 1160
            +Y PFG  GGGAP RD  G   T   G    N     + R    S+                         E + +  EL+   + G PKRDP+TG L N HL SSDV+  K+       P  P+E           Y   L +AA+ER+  K L+KLRERQE  +H + +++ WG
Sbjct:  368 IYDPFGKPGGGAPIRDRWGNRVTNIFG----NFEGKVQSRTEFISRLSNSMS-------------------EQDTELAELVRQGQVGNPKRDPITGALTNQHLGSSDVSKTKM----NYQPVAPSEKKQ--------YYETLTQAAEERERAKQLEKLRERQESNRHFEVFDHQWG 508
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BLAST of SMED30015561 vs. Ensembl Nematostella
Match: EDO42197 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S294])

HSP 1 Score: 57.3806 bits (137), Expect = 6.620e-9
Identity = 49/181 (27.07%), Postives = 84/181 (46.41%), Query Frame = 3 
Query:  627 VNLYFPFGSSGGGAPRRDNQGRIQTTFVGPEYLNVNI--DEKKRKILASKAIXXXXXXXXXXXXXXXXXXXXXNREPNG-DFTELISSFKGGRPKRDPLTGMLINNHLQSSDVTNMKLASPRATSPWIPNEMVSMSNVDTLTYGMELAKAAKERQVMKHLDKLRERQECKQHVDAWNNIWG 1160
            V  Y PFG  G GAP R   G ++T  +G    +  +  D   R   A+K       + M ++   + + +++  +  G D    +     G+P+ DP+TG ++ +H  +SD+T  KL   R       NE+       +  Y  +L + A+ER+  K   +  E +  ++HVD  N+IWG
Sbjct:  512 VECYNPFGRPGAGAPVRGADGTVKTHIMGKVEKDAVVLNDPSPRTDPATKHEYLQTLRNMTEEAREQRKAEKEELKTGGADVAAWLRKGVIGQPQYDPVTGEIVASHKHTSDITQQKLNIRRQK-----NEL-------SQQYHQDLERLAQEREKDKVQRRDLEHRHSREHVDTMNSIWG 680
The following BLAST results are available for this feature:
BLAST of SMED30015561 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 SMED30015561 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 SMED30015561 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 SMED30015561 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 SMED30015561 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 SMED30015561 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 SMED30015561 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 SMED30015561 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267F9W56.479e-1937.04Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8FTN01.111e-1837.04Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267GWT61.145e-1837.04Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A433T2W72.155e-1230.68Uncharacterized protein OS=Elysia chlorotica OX=18... [more]
A0A2T7PR825.531e-1232.95Uncharacterized protein OS=Pomacea canaliculata OX... [more]
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BLAST of SMED30015561 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 SMED30015561 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 SMED30015561 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 SMED30015561 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO421976.620e-927.07Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30015561 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 SMED30015561 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015561 ID=SMED30015561|Name=SMED30015561|organism=Schmidtea mediterranea sexual|type=transcript|length=1318bp
CCATATGGTAACGTTAAATACTGGCAAATTTAACCTTATAAAAAGCATTT
AGTTTTTCATAGTATTTAATTCATATGAATTTTTACGGAGAATCTAGCCC
AGTTAATTTAGCATTTCAAAATGTCAATGATAATAACCAGAAAATAGCTA
CTGTCCTTCCACCGTATCCGGAATCTCATTCCAACCATAATATAAATGAT
ATGGAATTTGACAACCTGAAAGAATTTCGTTCCAGAATACTAGAAATGGA
CGACGAAATAAAACAATTGAAAAATATTGAACGTGAAAAACAGTTTCAAC
AGAAAAATGAATATCAAGTACATGATAGTCAATCAAAATCAAAAATATTT
CTCAAAGACGAAGCTGTATCCACGACAGAAACATTGCTACAAGAACAAAC
AAATCGTATTGCCGAATTGGAACGTGATTTTCAAGAGTTGAAAAGAAATG
CTAACTTTAAACAAAATAGTACACGGCTGAATGAAAATTCCCAAGAAAAC
CGAAACTTTGATTTTGGAAATGAAAATACTAATCGCAAAAAATTCGAATA
TGGAAAAGAATTCGAAGATGATGTGAATCACAGAATTGGTAATTGGACAC
CTAAAGATCCCTACCAAGGGCCTATGGTGAATCTTTATTTTCCATTTGGT
TCCTCTGGCGGTGGAGCTCCAAGAAGAGATAATCAAGGTCGTATACAAAC
AACATTCGTTGGTCCAGAGTATTTAAACGTAAATATTGACGAGAAAAAGC
GCAAAATTTTAGCGTCTAAAGCAATTCAAGAATCACAGCAACAAGAAATG
TTGCAACAAAGATTGAGAAGATTACAAGATAAGCAGCAAAATCGTGAACC
AAATGGAGATTTCACTGAACTTATTTCAAGTTTTAAAGGTGGTCGGCCAA
AACGAGATCCTTTAACCGGGATGCTGATAAACAATCATTTACAATCAAGT
GATGTTACAAACATGAAATTGGCTTCACCTAGAGCTACATCACCGTGGAT
ACCAAATGAGATGGTTTCAATGTCAAATGTTGACACATTAACATACGGAA
TGGAGTTAGCTAAGGCTGCAAAGGAGAGACAAGTGATGAAACATTTAGAC
AAACTGAGAGAACGGCAAGAATGCAAACAACATGTCGACGCATGGAACAA
TATATGGGGCCCAAGAGAAAGATATGAACCGAATTTCACATATTCGAATG
TCACAAGCAATCACCGCAATTTTTATCAATTACCAAAATAAAAATTCTGA
CCGAATTTCTTTTGTTAACATGTTGTTCTCTCTGATGAGGAAAATTTAAT
TTTTATTTCTAAAATATA
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protein sequence of SMED30015561-orf-1

>SMED30015561-orf-1 ID=SMED30015561-orf-1|Name=SMED30015561-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=389bp
MNFYGESSPVNLAFQNVNDNNQKIATVLPPYPESHSNHNINDMEFDNLKE
FRSRILEMDDEIKQLKNIEREKQFQQKNEYQVHDSQSKSKIFLKDEAVST
TETLLQEQTNRIAELERDFQELKRNANFKQNSTRLNENSQENRNFDFGNE
NTNRKKFEYGKEFEDDVNHRIGNWTPKDPYQGPMVNLYFPFGSSGGGAPR
RDNQGRIQTTFVGPEYLNVNIDEKKRKILASKAIQESQQQEMLQQRLRRL
QDKQQNREPNGDFTELISSFKGGRPKRDPLTGMLINNHLQSSDVTNMKLA
SPRATSPWIPNEMVSMSNVDTLTYGMELAKAAKERQVMKHLDKLRERQEC
KQHVDAWNNIWGPRERYEPNFTYSNVTSNHRNFYQLPK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000035Category 3 cell
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 48..78
NoneNo IPR availableCOILSCoilCoilcoord: 233..253
NoneNo IPR availableCOILSCoilCoilcoord: 98..132