SMED30008243

Overview
NameSMED30008243
Smed IDSMED30008243
Length (bp)609
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 SMED30008243 (SMED30008243) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008243 (SMED30008243) 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 SMED30008243 (SMED30008243) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008243 (SMED30008243) 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




SMED30008243

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
gutSMED30008243SMESG000062646.1 dd_Smed_v4_2042_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30008243SMESG000062646.1 dd_Smed_v4_2042_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30008243SMESG000062646.1 dd_Smed_v4_2042_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30008243SMESG000062646.1 dd_Smed_v4_2042_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30008243SMESG000062646.1 dd_Smed_v4_2042_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008243SMESG000062646.1 Contig51653newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008243SMESG000062646.1 Contig51653uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30008243SMESG000062646.1 dd_Smed_v4_2042_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
SMED30008243 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004703:13759..16169 +2818
Homology
BLAST of SMED30008243 vs. TrEMBL
Match: A0A1S3JXA5 (uncharacterized protein LOC106176901 OS=Lingula unguis OX=7574 GN=LOC106176901 PE=4 SV=1)

HSP 1 Score: 87.8113 bits (216), Expect = 2.372e-18
Identity = 51/134 (38.06%), Postives = 83/134 (61.94%), Query Frame = 1
Query:  118 DAIYHSKYRYVTPVL----NVFGFITGLMMLLSFILSLVQGHAVKWEFYLLXXXXXXXXXXXXXXXWWYHMGDMPKEKFWILVMLFAIVIFQCISTDIYIFHT----NDIPSQSTTAPKNPTTISSKFHNITGR 495
            +AIYH     V+P L     VFG +T LM++++FI+ LV G A    FYL+  N++IS+ +  ++ WWY  GD+  +K W ++++ A+++FQCI+T+IY+F+     NDIP+     P  P   ++  HN+T R
Sbjct:   19 NAIYHD----VSPTLIYGSKVFGVVTCLMVIIAFIICLVTG-AKNNTFYLMATNLLISTFVGAVVTWWYRKGDLASDKIWFIILVCAVIVFQCITTEIYVFNVQYVHNDIPT-----PAPPRINTTAHHNMTTR 142          
BLAST of SMED30008243 vs. TrEMBL
Match: A0A1S3JXZ7 (uncharacterized protein LOC106176894 OS=Lingula unguis OX=7574 GN=LOC106176894 PE=4 SV=1)

HSP 1 Score: 85.5001 bits (210), Expect = 1.543e-17
Identity = 48/130 (36.92%), Postives = 82/130 (63.08%), Query Frame = 1
Query:  118 DAIYHSKYRYVTPVL----NVFGFITGLMMLLSFILSLVQGHAVKWEFYLLXXXXXXXXXXXXXXXWWYHMGDMPKEKFWILVMLFAIVIFQCISTDIYIFHTNDIPSQSTTAPKNPTTISSKFHNITGR 495
            +AIYH     V+P L     VFG +T LM++++FI+ LV G A    FYL+  N++IS+ +  ++ WWY  GD+  +K W ++++ A+++FQCI+T+IY+F+   + +  +T P  P   ++  HN+T R
Sbjct:   19 NAIYHD----VSPTLIYGSKVFGVVTCLMVVIAFIICLVTG-AKNNTFYLMATNLLISTFVGAVVTWWYRKGDLASDKIWFIILVCAVIVFQCITTEIYVFNVQYVDNDVST-PAPPRINTTAHHNMTTR 142          
BLAST of SMED30008243 vs. TrEMBL
Match: A0A210PMT5 (Uncharacterized protein OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT06001 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 3.360e-13
Identity = 39/100 (39.00%), Postives = 65/100 (65.00%), Query Frame = 1
Query:  115 EDAIYHSKYRYVTPVLNVFGFITGLMMLLSFILSLVQGHAVKWEFYLLXXXXXXXXXXXXXXXWWYHMGDMPKEKFWILVMLFAIVIFQCISTDIYIFHT 414
             +AIYH     +T +L     I  LM+++SF + LV+GH  +  FYLL  N VIS+++  ++ WWY  GD+  +K+W + ++ A++ FQCI+TD+Y+F +
Sbjct:   10 SNAIYHEVPPTITFLLRFCNVIMALMIVISFTMCLVEGHRNQ-TFYLLACNTVISALVGVVVNWWYRGGDLGSDKYWYIFIVAAVITFQCITTDVYLFKS 108          
BLAST of SMED30008243 vs. TrEMBL
Match: A0A2C9JRU5 (Uncharacterized protein OS=Biomphalaria glabrata OX=6526 GN=106065465 PE=4 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 1.761e-11
Identity = 35/102 (34.31%), Postives = 63/102 (61.76%), Query Frame = 1
Query:  115 EDAIYHSKYRYVTPVLNVFGFITGLMMLLSFILSLVQGHAVKWEFYLLXXXXXXXXXXXXXXXWWYHMGDMPKEKFWILVMLFAIVIFQCISTDIYIFHTND 420
            E A++H        ++ +   IT +M+L++ I   VQGH   + +YLL  N++IS ++  ++ WWY  GD+  EK+W +++L  +++FQCISTD ++F  + 
Sbjct:   10 EKAVFHEINPRTVLIVRIVNAITLIMILIAVIACFVQGHKNSF-YYLLVCNLIISILVYLVVNWWYRTGDLGSEKYWFVLLLNVVILFQCISTDTFVFKVDS 110          
BLAST of SMED30008243 vs. TrEMBL
Match: A0A0B6YAF8 (Uncharacterized protein (Fragment) OS=Arion vulgaris OX=1028688 GN=ORF19364 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 2.957e-10
Identity = 40/131 (30.53%), Postives = 79/131 (60.31%), Query Frame = 1
Query:  100 DLDKVED-AIYHSKYRYVTPVLNVFGFITGLMMLLSFILSLVQGHAVKWEFYLLXXXXXXXXXXXXXXXWWYHMGDMPKEKFWILVMLFAIVIFQCISTDIYIFHTNDIPSQSTTAPKNPTTISSKFHNIT 489
            ++ KV+  AI+H     +  ++ +   IT +M++++ +L +VQG      +YLL  N+VIS ++  ++ WWY  GD+  EK+W ++++ A++  QCI++D+Y++   ++P  +TT       IS+   N+T
Sbjct:    8 NVTKVDSGAIFHELNPKLIWLVRIVNIITLVMVIIAVVLCIVQGSKENASYYLLVCNLVISGLVCIVVNWWYRNGDLGSEKYWFILLVGAVIFLQCITSDLYVYKDEEVPVTTTTTVATTQFISTTNRNLT 138          
BLAST of SMED30008243 vs. Ensembl Nematostella
Match: EDO30494 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7T0M4])

HSP 1 Score: 45.0542 bits (105), Expect = 1.407e-6
Identity = 30/101 (29.70%), Postives = 59/101 (58.42%), Query Frame = 1
Query:  115 EDAIYHSKYRYVTPVLNVFGFIT--GLMMLLSFILSLVQGHAVKWEFYLLXXXXXXXXXXXXXXXWWYHMGDMPKEKFWILVMLFAIVIFQCISTDIYIFH 411
             D ++H K +     L ++ FI+   +MM+++ I++L +G  V   + LLG++I+    + GI+++W   GD+P EK W L  +   ++ + I TD+ ++H
Sbjct:   17 SDPLFHDKGQSPKAKLWMYIFISFVVVMMMITIIIALFRGSVVDATYLLLGLSIISMGFVQGILIYWARSGDLPSEKLWFLYFVGICLVLESIFTDVLLYH 117          
BLAST of SMED30008243 vs. Planmine SMEST
Match: SMESG000062646.1 (SMESG000062646.1)

HSP 1 Score: 255.758 bits (652), Expect = 5.240e-88
Identity = 141/142 (99.30%), Postives = 141/142 (99.30%), Query Frame = 1
Query:   88 MYGSDLDKVEDAIYHSKYRYVTPVLNVFGFITGLMMLLSFILSLVQGHAVKWEFYLLXXXXXXXXXXXXXXXWWYHMGDMPKEKFWILVMLFAIVIFQCISTDIYIFHTNDIPSQSTTAPKNPTTISSKFHNITGRAFLALS 513
            MYGSDLDKVEDAIYHSKYRYVTPVLNVFGFITGLMMLLSFILSLVQGHAVKWEFYLLGVNIVISSIIVGIIVWWYHMGDMPKEKFWILVMLFAIVIFQCISTDIYIFHTNDIPSQSTTAPKNPTTISSKFHNITG AFLALS
Sbjct:    1 MYGSDLDKVEDAIYHSKYRYVTPVLNVFGFITGLMMLLSFILSLVQGHAVKWEFYLLGVNIVISSIIVGIIVWWYHMGDMPKEKFWILVMLFAIVIFQCISTDIYIFHTNDIPSQSTTAPKNPTTISSKFHNITGHAFLALS 142          
The following BLAST results are available for this feature:
BLAST of SMED30008243 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 SMED30008243 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 SMED30008243 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 SMED30008243 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 SMED30008243 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 SMED30008243 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 SMED30008243 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 SMED30008243 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1S3JXA52.372e-1838.06uncharacterized protein LOC106176901 OS=Lingula un... [more]
A0A1S3JXZ71.543e-1736.92uncharacterized protein LOC106176894 OS=Lingula un... [more]
A0A210PMT53.360e-1339.00Uncharacterized protein OS=Mizuhopecten yessoensis... [more]
A0A2C9JRU51.761e-1134.31Uncharacterized protein OS=Biomphalaria glabrata O... [more]
A0A0B6YAF82.957e-1030.53Uncharacterized protein (Fragment) OS=Arion vulgar... [more]
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BLAST of SMED30008243 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 SMED30008243 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 SMED30008243 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 SMED30008243 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO304941.407e-629.70Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30008243 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 SMED30008243 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000062646.15.240e-8899.30SMESG000062646.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008243 ID=SMED30008243|Name=SMED30008243|organism=Schmidtea mediterranea sexual|type=transcript|length=609bp
CAACTCCATAAATTGATTGATTTTGAGTTAAATAATCCGATTTTAATAAT
CTTTTAATTTATTTCAATTAATAATTTTATTAATAATATGTATGGGTCGG
ATCTAGATAAGGTGGAGGACGCCATTTATCACAGTAAATACCGATATGTG
ACTCCTGTTTTAAATGTTTTCGGATTCATAACCGGACTCATGATGCTTCT
GTCATTCATTTTGTCTCTGGTTCAAGGTCACGCGGTAAAGTGGGAGTTTT
ATTTGCTGGGAGTAAACATTGTCATTTCTAGTATAATTGTCGGTATAATA
GTTTGGTGGTATCATATGGGAGATATGCCAAAGGAGAAGTTTTGGATTCT
CGTTATGTTATTTGCTATTGTGATATTTCAGTGTATCTCTACAGATATTT
ACATATTCCACACAAACGACATTCCTTCACAGAGTACTACTGCACCAAAA
AATCCAACAACAATTAGCTCAAAATTTCATAATATTACTGGACGCGCATT
CCTTGCATTGAGTTGATTGGGGCGCCGATGAAAATTTGAAGATTTTACTG
TTTTATCCTTCGATTTTAAAAAAATATATTTTTTCTTTTTAAAAAAAAAG
ATCGGAAGA
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protein sequence of SMED30008243-orf-1

>SMED30008243-orf-1 ID=SMED30008243-orf-1|Name=SMED30008243-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
MYGSDLDKVEDAIYHSKYRYVTPVLNVFGFITGLMMLLSFILSLVQGHAV
KWEFYLLGVNIVISSIIVGIIVWWYHMGDMPKEKFWILVMLFAIVIFQCI
STDIYIFHTNDIPSQSTTAPKNPTTISSKFHNITGRAFLALS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 86..108
NoneNo IPR availableTMHMMTMhelixcoord: 54..76
NoneNo IPR availableTMHMMTMhelixcoord: 20..42