SMED30000603

Overview
NameSMED30000603
Smed IDSMED30000603
Length (bp)853
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30000603 (SMED30000603) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000603 (SMED30000603) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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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Homology
BLAST of SMED30000603 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 313.153 bits (801), Expect = 3.685e-97
Identity = 149/159 (93.71%), Postives = 155/159 (97.48%), Query Frame = 3
Query:  147 MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDVASISSLYPDELCILIKLINIDEEVTTEKIYEILFMRLEIAEFGKEWSIMMKKVETMEDEIMRMIKEQTKVYRECYVCRTEEARVMVIPCGHLSFCQGCARESHCVLCQRKIKERITVFYP 623
            MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKED+ASISSLYPDELC LIKLINIDEEV TE+IYEIL MRLEIAEFGKEWSIMM+KVET+EDEIMRM+KEQTK YRECYVCRTEEARVMVIPCGHLSFCQGCA+ESHCVLCQRKIKERITVFYP
Sbjct: 2359 MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDLASISSLYPDELCTLIKLINIDEEVITERIYEILLMRLEIAEFGKEWSIMMEKVETIEDEIMRMMKEQTKAYRECYVCRTEEARVMVIPCGHLSFCQGCAKESHCVLCQRKIKERITVFYP 2517          
BLAST of SMED30000603 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 312.383 bits (799), Expect = 6.940e-97
Identity = 149/159 (93.71%), Postives = 155/159 (97.48%), Query Frame = 3
Query:  147 MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDVASISSLYPDELCILIKLINIDEEVTTEKIYEILFMRLEIAEFGKEWSIMMKKVETMEDEIMRMIKEQTKVYRECYVCRTEEARVMVIPCGHLSFCQGCARESHCVLCQRKIKERITVFYP 623
            MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKED+ASISSLYPDELC LIKLINIDEEV TE+IYEIL MRLEIAEFGKEWSIMM+KVET+EDEIMRM+KEQTK YRECYVCRTEEARVMVIPCGHLSFCQGCA+ESHCVLCQRKIKERITVFYP
Sbjct: 2519 MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDLASISSLYPDELCTLIKLINIDEEVITERIYEILLMRLEIAEFGKEWSIMMEKVETIEDEIMRMMKEQTKAYRECYVCRTEEARVMVIPCGHLSFCQGCAKESHCVLCQRKIKERITVFYP 2677          
BLAST of SMED30000603 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 311.997 bits (798), Expect = 8.250e-97
Identity = 149/159 (93.71%), Postives = 155/159 (97.48%), Query Frame = 3
Query:  147 MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDVASISSLYPDELCILIKLINIDEEVTTEKIYEILFMRLEIAEFGKEWSIMMKKVETMEDEIMRMIKEQTKVYRECYVCRTEEARVMVIPCGHLSFCQGCARESHCVLCQRKIKERITVFYP 623
            MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKED+ASISSLYPDELC LIKLINIDEEV TE+IYEIL MRLEIAEFGKEWSIMM+KVET+EDEIMRM+KEQTK YRECYVCRTEEARVMVIPCGHLSFCQGCA+ESHCVLCQRKIKERITVFYP
Sbjct: 2490 MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDLASISSLYPDELCTLIKLINIDEEVITERIYEILLMRLEIAEFGKEWSIMMEKVETIEDEIMRMMKEQTKAYRECYVCRTEEARVMVIPCGHLSFCQGCAKESHCVLCQRKIKERITVFYP 2648          
BLAST of SMED30000603 vs. Planmine SMEST
Match: SMESG000065358.1 (SMESG000065358.1)

HSP 1 Score: 244.202 bits (622), Expect = 1.664e-77
Identity = 114/159 (71.70%), Postives = 140/159 (88.05%), Query Frame = 3
Query:  147 MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDVASISSLYPDELCILIKLINIDEEVTTEKIYEILFMRLEIAEFGKEWSIMMKKVETMEDEIMRMIKEQTKVYRECYVCRTEEARVMVIPCGHLSFCQGCARESHCVLCQRKIKERITVFYP 623
            ME TK II KL+ ILNIENDNLE LINKQKL+++ KED+++IS+LY DE CILIKLI+ID++VTTE+IYEILFMRLEI +FGK W+ +M+KV+ +EDEI   +KEQTK Y ECY C+TEEARVMVIPCGHLS+C GCA+ESHC+LCQRKIKER+TV++P
Sbjct:  343 MEPTK-IIEKLKGILNIENDNLEELINKQKLIKRAKEDISTISNLYSDEHCILIKLIDIDKDVTTERIYEILFMRLEITKFGKSWNKLMEKVKNIEDEIATTMKEQTKAYVECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIKERLTVYFP 500          
BLAST of SMED30000603 vs. Planmine SMEST
Match: SMESG000039477.1 (SMESG000039477.1)

HSP 1 Score: 237.654 bits (605), Expect = 6.864e-77
Identity = 112/159 (70.44%), Postives = 137/159 (86.16%), Query Frame = 3
Query:  147 MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDVASISSLYPDELCILIKLINIDEEVTTEKIYEILFMRLEIAEFGKEWSIMMKKVETMEDEIMRMIKEQTKVYRECYVCRTEEARVMVIPCGHLSFCQGCARESHCVLCQRKIKERITVFYP 623
            ME TK II KL+ ILNIENDNLE LINKQKL+++ KED+++IS+LY DE CILIKL +ID+++TTE+IYEIL MRLEI +FGK W+ +MKK E +EDEI   +KEQTK Y ECY C+TEEARVMVIPCGHLS+C GCA+ESHC+LCQRKIKER+TV++P
Sbjct:  186 MEPTK-IIEKLKGILNIENDNLEELINKQKLIKRAKEDISTISNLYSDEHCILIKLSDIDKDITTERIYEILSMRLEITKFGKSWNKLMKKAENIEDEIATTMKEQTKAYLECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIKERLTVYFP 343          
The following BLAST results are available for this feature:
BLAST of SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 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 SMED30000603 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000052862.13.685e-9793.71SMESG000052862.1[more]
SMESG000052862.16.940e-9793.71SMESG000052862.1[more]
SMESG000052862.18.250e-9793.71SMESG000052862.1[more]
SMESG000065358.11.664e-7771.70SMESG000065358.1[more]
SMESG000039477.16.864e-7770.44SMESG000039477.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000603 ID=SMED30000603|Name=SMED30000603|organism=Schmidtea mediterranea sexual|type=transcript|length=853bp
TGAAAATGGGGAAAGTTAAGAGAACGAAAGTAAAAATAAATAGAATAGAA
AAGAATTTAAACGGGGAAAAATCAAATGAACCCAACGTGAGAATAAGCGA
TAATAAATTAATATAAGGACCATATTGATTAATGTTTTATTAATAGATGG
AGCAAACTAAACCGATAATAACGAAACTAAGAGAGATACTGAACATCGAA
AATGACAACCTAGAGAGATTGATAAATAAACAAAAATTAATGAGAAAAGT
TAAAGAAGACGTCGCATCGATTTCAAGCCTCTACCCTGATGAACTATGTA
TTCTGATAAAATTAATTAACATCGACGAAGAAGTAACAACCGAAAAGATA
TATGAAATTTTGTTTATGAGATTGGAGATAGCCGAATTTGGCAAAGAGTG
GAGCATAATGATGAAAAAGGTCGAAACAATGGAAGATGAGATAATGCGAA
TGATAAAAGAGCAAACCAAAGTCTATCGGGAATGTTATGTATGTCGAACG
GAAGAAGCACGAGTGATGGTAATACCTTGTGGGCACTTGAGTTTTTGTCA
GGGGTGTGCCAGAGAGTCGCATTGTGTGTTATGTCAGAGAAAGATAAAGG
AACGAATTACAGTGTTTTATCCATGAAATTGTAGTAGTAATCGATAATAA
ATGAGTTGTTGTAATAGTTAATAATTAAATGTATAATGTGTGTAAAAGAG
TAACTGATAAATAGGAATAAACAAATGACGACAAGAAAAATTAAAGTAAC
ATACGAAAGCCGAATCAGGGAAAAATTAATTACATGCACAGAGACACAAA
AGCAGCGGAATCTATCTAGACCGCATATTTGGACAGAAAAATTTCGACAA
CCA
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protein sequence of SMED30000603-orf-1

>SMED30000603-orf-1 ID=SMED30000603-orf-1|Name=SMED30000603-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=160bp
MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDVASISSLYPDEL
CILIKLINIDEEVTTEKIYEILFMRLEIAEFGKEWSIMMKKVETMEDEIM
RMIKEQTKVYRECYVCRTEEARVMVIPCGHLSFCQGCARESHCVLCQRKI
KERITVFYP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding
GO:0016874ligase activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 21..43