SMED30016134

Overview
NameSMED30016134
Smed IDSMED30016134
Length (bp)590
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 SMED30016134 (SMED30016134) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016134 (SMED30016134) 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 SMED30016134 (SMED30016134) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016134 (SMED30016134) 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




SMED30016134

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30016134SMESG000045543.1 dd_Smed_v4_2401_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30016134SMESG000045543.1 dd_Smed_v4_2401_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30016134SMESG000045543.1 dd_Smed_v4_2401_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30016134SMESG000045543.1 dd_Smed_v4_2401_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermal cellSMED30016134SMESG000045543.1 dd_Smed_v4_2401_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30016134 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003645:67535..68288 -2888
v31.013574:3544..4524 +2797
Homology
BLAST of SMED30016134 vs. TrEMBL
Match: A0A2T7PZK2 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_01463 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 1.907e-10
Identity = 39/128 (30.47%), Postives = 75/128 (58.59%), Query Frame = 1
Query:   88 MSSDNNPF-----------NTAHNDSSTPLFQDKATSPAVKKXXXXXXXXXXXXXXXXXXXXXYQGVRYKGNGFVFFMLGATLISYVVFEILIIVLIHRHKLEGNKRWYMILVAFAIITEAVFIDIVI 438
            MS++N P             T+   S + LF D + SP+ +   +    +++++V+I++ L+IY+GV    NGF++F+LG  LI + V EI++I+ + R  L   K W++ +V  A+I +++F ++V+
Sbjct:    1 MSAENQPILSGNGKPVSSTETSPVSSGSALFHDSSQSPSARLCQLLFVALVVLMVVISVVLSIYRGVVVNENGFMYFLLGLGLIGFAVLEIIMIMFVRRGDLPKGKTWFLYIVGGAVILQSIFTNVVL 128          
BLAST of SMED30016134 vs. TrEMBL
Match: A0A0L8FGV7 (Uncharacterized protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22022632mg PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 1.731e-7
Identity = 25/65 (38.46%), Postives = 41/65 (63.08%), Query Frame = 1
Query:  244 YQGVRYKGNGFVFFMLGATLISYVVFEILIIVLIHRHKLEGNKRWYMILVAFAIITEAVFIDIVI 438
            YQGV  + NG ++FMLG +LI +VV E+L++  I +  L   K W++  V   +  EA+F D+++
Sbjct:   54 YQGVHQQANGALYFMLGLSLIGFVVVELLMVNFIRKGDLSREKTWFLYFVGGCVFLEAIFTDVLL 118          
BLAST of SMED30016134 vs. TrEMBL
Match: A0A1S3JX16 (uncharacterized protein LOC106176852 OS=Lingula unguis OX=7574 GN=LOC106176853 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 2.447e-7
Identity = 32/103 (31.07%), Postives = 66/103 (64.08%), Query Frame = 1
Query:  130 SSTPLFQDKATSPAVKKXXXXXXXXXXXXXXXXXXXXXYQGVRYKGNGFVFFMLGATLISYVVFEILIIVLIHRHKLEGNKRWYMILVAFAIITEAVFIDIVI 438
            S+ PL+ D   +P ++ + +    +++++V+I+I L+I Q V+   N  V+ +LG +L+ + V E+++IV I + +L   + W++ +V F I+ EA+F DI++
Sbjct:   18 SAGPLYHDSTQTPLMRGLQLTFVSLVVLMVLISIILSIAQSVQVPMNTGVYLLLGISLLGFAVIEVILIVFIRQGELPKERMWFLYVVGFCILLEAIFTDILL 120          
BLAST of SMED30016134 vs. TrEMBL
Match: A0A3S1BJ58 (Uncharacterized protein OS=Elysia chlorotica OX=188477 GN=EGW08_010170 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 2.579e-7
Identity = 34/108 (31.48%), Postives = 65/108 (60.19%), Query Frame = 1
Query:  115 TAHNDSSTPLFQDKATSPAVKKXXXXXXXXXXXXXXXXXXXXXYQGVRYKGNGFVFFMLGATLISYVVFEILIIVLIHRHKLEGNKRWYMILVAFAIITEAVFIDIVI 438
            T  + S+  ++ D + +P  + + +    ++ ++V+IT+SL+IY+ +    NG ++FMLG  L+ +V+ EIL+IV   R  L   K W++  V   ++ EA+F DI++
Sbjct:   27 TVSSSSADAIYHDSSQTPRSRLVQVLFVALVAVMVVITLSLSIYRSIDVTYNGGMYFMLGVCLLGFVIIEILMIVFTRRGDLPKGKTWFLYFVGVCVLFEALFTDILL 134          
BLAST of SMED30016134 vs. TrEMBL
Match: A0A2C9KWS2 (Uncharacterized protein OS=Biomphalaria glabrata OX=6526 GN=106050262 PE=4 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 7.175e-7
Identity = 33/111 (29.73%), Postives = 66/111 (59.46%), Query Frame = 1
Query:  106 PFNTAHNDSSTPLFQDKATSPAVKKXXXXXXXXXXXXXXXXXXXXXYQGVRYKGNGFVFFMLGATLISYVVFEILIIVLIHRHKLEGNKRWYMILVAFAIITEAVFIDIVI 438
            P   +   +   ++ D A SP  + + I    +++++V+++ISL+IY+G   K NG ++FML  +L+ + + EI++I+   R  L   K W++  V F I+ E++F D+++
Sbjct:   19 PVANSSEVTDEAVYHDSAQSPTSRFLQILFVGLVVVMVLVSISLSIYRGSDVKENGGMYFMLAISLVGFALVEIIMIIFTRRGDLPKGKTWFLYFVGFCIMLESIFTDVLV 129          
BLAST of SMED30016134 vs. Planmine SMEST
Match: SMESG000045543.1 (SMESG000045543.1)

HSP 1 Score: 192.586 bits (488), Expect = 1.341e-63
Identity = 118/119 (99.16%), Postives = 119/119 (100.00%), Query Frame = 1
Query:   88 MSSDNNPFNTAHNDSSTPLFQDKATSPAVKKXXXXXXXXXXXXXXXXXXXXXYQGVRYKGNGFVFFMLGATLISYVVFEILIIVLIHRHKLEGNKRWYMILVAFAIITEAVFIDIVIMS 444
            MSSDNNPFNTA+NDSSTPLFQDKATSPAVKKINIAITVVLIIIVIITISLAIYQGVRYKGNGFVFFMLGATLISYVVFEILIIVLIHRHKLEGNKRWYMILVAFAIITEAVFIDIVIMS
Sbjct:    1 MSSDNNPFNTAYNDSSTPLFQDKATSPAVKKINIAITVVLIIIVIITISLAIYQGVRYKGNGFVFFMLGATLISYVVFEILIIVLIHRHKLEGNKRWYMILVAFAIITEAVFIDIVIMS 119          
The following BLAST results are available for this feature:
BLAST of SMED30016134 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 SMED30016134 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 SMED30016134 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 SMED30016134 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 SMED30016134 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 SMED30016134 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 SMED30016134 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 SMED30016134 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2T7PZK21.907e-1030.47Uncharacterized protein OS=Pomacea canaliculata OX... [more]
A0A0L8FGV71.731e-738.46Uncharacterized protein OS=Octopus bimaculoides OX... [more]
A0A1S3JX162.447e-731.07uncharacterized protein LOC106176852 OS=Lingula un... [more]
A0A3S1BJ582.579e-731.48Uncharacterized protein OS=Elysia chlorotica OX=18... [more]
A0A2C9KWS27.175e-729.73Uncharacterized protein OS=Biomphalaria glabrata O... [more]
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BLAST of SMED30016134 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 SMED30016134 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 SMED30016134 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 SMED30016134 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 SMED30016134 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 SMED30016134 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000045543.11.341e-6399.16SMESG000045543.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016134 ID=SMED30016134|Name=SMED30016134|organism=Schmidtea mediterranea sexual|type=transcript|length=590bp
AAAATGTTTTTCGCGGGTAATTGAAAATCACAATTTATTTAAAACTAATA
ATTTCCTAAATTGTTATTGCTCAAGTAATTTTTTGTCATGTCATCCGACA
ACAATCCTTTTAATACAGCTCATAATGACTCATCAACTCCGTTATTTCAA
GACAAAGCTACTTCACCAGCTGTGAAGAAAATAAACATTGCAATAACAGT
AGTTTTAATAATAATTGTGATTATCACTATCAGTCTGGCTATTTACCAAG
GCGTGCGATATAAAGGAAATGGATTTGTATTTTTTATGCTGGGGGCTACG
TTAATAAGCTATGTGGTTTTTGAAATATTAATTATCGTATTGATTCACCG
ACATAAACTAGAAGGCAACAAGCGCTGGTACATGATATTAGTCGCTTTTG
CTATAATTACTGAAGCAGTTTTCATTGATATTGTCATAATGTCTTAGAAA
TTTTTTATTTTTTTATATACCATTTTAGTCCATTTCTATTGGATAATTTC
ATCTTTGAATTTTTTAAAGAATAATTTGATGTTTTTGTGATTTTTTCATA
CTTATTAAAGAATTTCAGAAAGTAAATATTTATTTTTGTG
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protein sequence of SMED30016134-orf-1

>SMED30016134-orf-1 ID=SMED30016134-orf-1|Name=SMED30016134-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
MSSDNNPFNTAHNDSSTPLFQDKATSPAVKKINIAITVVLIIIVIITISL
AIYQGVRYKGNGFVFFMLGATLISYVVFEILIIVLIHRHKLEGNKRWYMI
LVAFAIITEAVFIDIVIMS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 64..86
NoneNo IPR availableTMHMMTMhelixcoord: 99..118
NoneNo IPR availableTMHMMTMhelixcoord: 32..54