SMED30018088

Overview
NameSMED30018088
Smed IDSMED30018088
Length (bp)385
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 SMED30018088 (SMED30018088) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018088 (SMED30018088) 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 SMED30018088 (SMED30018088) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018088 (SMED30018088) 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



SMED30018088

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30018088SMESG000068428.1 Contig52377newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018088SMESG000068428.1 Contig52377uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018088SMESG000068428.1 Contig9294newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018088SMESG000068428.1 Contig9294uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018088SMESG000068429.1 SMESG000068428.1 Contig21199newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018088SMESG000068429.1 SMESG000068428.1 Contig21199uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Category 3 cellSMED30018088SMESG000068428.1 dd_Smed_v6_343_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018088 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000820:10199..10583 -1871
v31.000820:11312..11696 -1862
v31.000820:11966..12345 -1129
Homology
[Close]
BLAST of SMED30018088 vs. Planmine SMEST
Match: SMESG000068428.1 (SMESG000068428.1)

HSP 1 Score: 130.954 bits (328), Expect = 3.680e-36
Identity = 115/118 (97.46%), Postives = 116/118 (98.31%), Query Frame = 2 
Query:    2 SNEFEAEDEDDFMKRAVTSKHPKTKKRNKPVTSXXXXXXXXXXXXXXXXXXXXXXXXXXXQTPRSXXXXXXXXXXXXXXRGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISN 355
            SNEFEAEDED+FMKRAVTSKHPKTKKRNKPVTSKVLTVKPTKYTPKTVTVKPTKSISKSTQTPRSDELDDGDEEEDILERGFTKRKSTTVKPATH KK GTIKPIIPTKKVGKRSISN
Sbjct:  433 SNEFEAEDEDNFMKRAVTSKHPKTKKRNKPVTSKVLTVKPTKYTPKTVTVKPTKSISKSTQTPRSDELDDGDEEEDILERGFTKRKSTTVKPATHTKKVGTIKPIIPTKKVGKRSISN 550

HSP 2 Score: 130.954 bits (328), Expect = 3.680e-36
Identity = 115/118 (97.46%), Postives = 116/118 (98.31%), Query Frame = 2 
Query:    2 SNEFEAEDEDDFMKRAVTSKHPKTKKRNKPVTSXXXXXXXXXXXXXXXXXXXXXXXXXXXQTPRSXXXXXXXXXXXXXXRGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISN 355
            SNEFEAEDED+FMKRAVTSKHPKTKKRNKPVTSKVLTVKPTKYTPKTVTVKPTKSISKSTQTPRSDELDDGDEEEDILERGFTKRKSTTVKPATH KK GTIKPIIPTKKVGKRSISN
Sbjct:  855 SNEFEAEDEDNFMKRAVTSKHPKTKKRNKPVTSKVLTVKPTKYTPKTVTVKPTKSISKSTQTPRSDELDDGDEEEDILERGFTKRKSTTVKPATHTKKVGTIKPIIPTKKVGKRSISN 972

HSP 3 Score: 73.1738 bits (178), Expect = 5.491e-16
Identity = 44/49 (89.80%), Postives = 47/49 (95.92%), Query Frame = 2 
Query:  239 RGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISNXXXXXXXXDF 385
            RG T+RKSTTVKPATH KKAGTIKPIIPTKKVGKRSISNEF+EEAE+DF
Sbjct:  294 RGLTQRKSTTVKPATHTKKAGTIKPIIPTKKVGKRSISNEFDEEAEDDF 342

HSP 4 Score: 72.7886 bits (177), Expect = 7.065e-16
Identity = 58/121 (47.93%), Postives = 63/121 (52.07%), Query Frame = 2 
Query:    2 SNEFEAEDEDDFMKRAVTSKHPKTKKRN---KPVTSXXXXXXXXXXXXXXXXXXXXXXXXXXXQTPRSXXXXXXXXXXXXXXRGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISN 355
            SNEF+ E EDDFMKRAV      TKK+N   KP T            P     K + S     +                  R  TK+KSTTVKPATH KK GTIKPIIPTKKVGKRSISN
Sbjct:  753 SNEFDEEAEDDFMKRAV------TKKKNTTVKPATHTKKVGTVKPIIPTRKVGKRSISNEFEEEAEEDFMK-----------RAVTKKKSTTVKPATHTKKVGTIKPIIPTKKVGKRSISN 856

HSP 5 Score: 72.4034 bits (176), Expect = 9.729e-16
Identity = 67/131 (51.15%), Postives = 78/131 (59.54%), Query Frame = 2 
Query:    2 SNEFEAEDEDDFMKRAVTSKHPKTKKRN---KPVTSXXXXXXXXXXXXXXXXXXXXXXXXXXXQTPRSXXXXXXXXXXXXXXRGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISNXXXXXXXXDF 385
            SNEF+ E EDDFMKRAV      TKK+N   KP T            P     K + S     +            E+D ++R  TK+K+TTVKPATH KK GT+KPIIPT+KVGKRSISNEFEEEAEEDF
Sbjct:  702 SNEFDEEAEDDFMKRAV------TKKKNTTVKPATHTKKVGTIKPIIPTKKVGKRSISNEFDEE-----------AEDDFMKRAVTKKKNTTVKPATHTKKVGTVKPIIPTRKVGKRSISNEFEEEAEEDF 815

HSP 6 Score: 72.4034 bits (176), Expect = 1.104e-15
Identity = 59/121 (48.76%), Postives = 67/121 (55.37%), Query Frame = 2 
Query:    2 SNEFEAEDEDDFMKRAVTSKHPKTKKRN---KPVTSXXXXXXXXXXXXXXXXXXXXXXXXXXXQTPRSXXXXXXXXXXXXXXRGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISN 355
            SNEF+ E EDDFMKRAVT      KK+N   KP T            P     K + S     +            E D ++R  TK+K+TTVKPATH KK GTIKPIIPTKKVGKRSISN
Sbjct:  331 SNEFDEEAEDDFMKRAVT------KKKNTTVKPATHTKKVGTIKPIIPTKKVGKRSISNEFEAE-----------LENDFMKRAVTKKKNTTVKPATHTKKVGTIKPIIPTKKVGKRSISN 434

HSP 7 Score: 68.5514 bits (166), Expect = 2.226e-14
Identity = 41/49 (83.67%), Postives = 43/49 (87.76%), Query Frame = 2 
Query:  239 RGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISNXXXXXXXXDF 385
            R  TK+KSTTVKPATH KK GTIKPIIPTKKVGKRSISNEFE + EEDF
Sbjct: 1087 RAVTKKKSTTVKPATHTKKVGTIKPIIPTKKVGKRSISNEFEAQEEEDF 1135

HSP 8 Score: 67.0106 bits (162), Expect = 7.404e-14
Identity = 40/49 (81.63%), Postives = 42/49 (85.71%), Query Frame = 2 
Query:  239 RGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISNXXXXXXXXDF 385
            R  TK+K+TTVKPATH KK GTIKPIIPTKKVGKRSISNEFE E E DF
Sbjct:  345 RAVTKKKNTTVKPATHTKKVGTIKPIIPTKKVGKRSISNEFEAELENDF 393

HSP 9 Score: 66.6254 bits (161), Expect = 1.123e-13
Identity = 41/49 (83.67%), Postives = 45/49 (91.84%), Query Frame = 2 
Query:  239 RGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISNXXXXXXXXDF 385
            R  TK+K+TTVKPATH KK GTIKPIIPTKKVGKRSISNEF+EEAE+DF
Sbjct:  665 RAVTKKKNTTVKPATHTKKVGTIKPIIPTKKVGKRSISNEFDEEAEDDF 713

HSP 10 Score: 64.6994 bits (156), Expect = 4.711e-13
Identity = 33/39 (84.62%), Postives = 35/39 (89.74%), Query Frame = 2 
Query:  239 RGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISN 355
            R  TK+K+TTVKPATH KK GTIKPIIPTKKVGKRSISN
Sbjct: 1036 RAVTKKKNTTVKPATHTKKVGTIKPIIPTKKVGKRSISN 1074

HSP 11 Score: 64.3142 bits (155), Expect = 8.183e-13
Identity = 32/39 (82.05%), Postives = 35/39 (89.74%), Query Frame = 2 
Query:  239 RGFTKRKSTTVKPATHKKKAGTIKPIIPTKKVGKRSISN 355
            R  TK+K+TTVKPATH KK GT+KPIIPTKKVGKRSISN
Sbjct:  614 RAVTKKKNTTVKPATHTKKVGTVKPIIPTKKVGKRSISN 652
The following BLAST results are available for this feature:
BLAST of SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 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 SMED30018088 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000068428.13.680e-3697.46SMESG000068428.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018088 ID=SMED30018088|Name=SMED30018088|organism=Schmidtea mediterranea sexual|type=transcript|length=385bp
TTCTAATGAATTTGAAGCAGAAGATGAAGATGATTTTATGAAACGAGCTG
TAACTAGTAAACATCCAAAAACCAAAAAAAGAAATAAACCTGTAACTTCT
AAAGTATTAACAGTAAAACCTACAAAATATACTCCAAAAACTGTCACAGT
CAAGCCAACTAAATCAATAAGCAAAAGTACGCAAACTCCACGTTCAGATG
AATTAGACGATGGTGATGAAGAGGAAGACATTTTGGAACGGGGCTTTACC
AAAAGGAAGAGTACCACTGTTAAACCAGCAACTCATAAGAAGAAAGCTGG
CACTATTAAACCGATCATTCCGACAAAGAAAGTGGGAAAGCGATCGATTT
CAAATGAATTTGAAGAAGAAGCAGAAGAAGATTTC
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protein sequence of SMED30018088-orf-1

>SMED30018088-orf-1 ID=SMED30018088-orf-1|Name=SMED30018088-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=128bp
SNEFEAEDEDDFMKRAVTSKHPKTKKRNKPVTSKVLTVKPTKYTPKTVTV
KPTKSISKSTQTPRSDELDDGDEEEDILERGFTKRKSTTVKPATHKKKAG
TIKPIIPTKKVGKRSISNEFEEEAEEDF
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..128
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 34..62
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 18..32