SMED30003180

Overview
NameSMED30003180
Smed IDSMED30003180
Length (bp)3460
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 SMED30003180 (SMED30003180) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003180 (SMED30003180) 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 SMED30003180 (SMED30003180) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003180 (SMED30003180) 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




SMED30003180

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testis primordiumSMED30003180SMESG000013216.1 Contig6552_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30003180 vs. Planmine SMEST
Match: SMESG000013216.1 (SMESG000013216.1)

HSP 1 Score: 424.476 bits (1090), Expect = 1.484e-138
Identity = 249/251 (99.20%), Postives = 251/251 (100.00%), Query Frame = -2
Query: 2293 MEVNINNTTSDLNPINYFTNKXXXXXXXXXXXSDEGLLPFAKQFQNSVDEKTYFSSTEDPSKPMVTNFTKTDRRLKMIENXXXXXXXXXXXXXKLIRGLPRRKVTIYSQKHEKIAAALSCIENAIPELLEKALFTEPLNCKTHNWPTANGLFIRQLRKSKFFHKRALNCPLGKSSWSNVIDPKKIFPFKTASFSLRTSVLHNTNKITSKNNISPINEDNDIIIEAQTEQTTDXXXXXXXXXXXXXYVMPKD 3045
            MEVNINNTTSDLNPINYFTNKYSFYSYFYPSESDEGLLPFAKQFQNSVDEKTYFSSTEDPSKPMVTNFTKTDRRLKMIENKCGVEIKIGGIE+KL+RGLPRRKVTIYSQKHEKIAAALSCIENAIPELLEKALFTEPLNCKTHNWPTANGLFIRQLRKSKFFHKRALNCPLGKSSWSNVIDPKKIFPFKTASFSLRTSVLHNTNKITSKNNISPINEDNDIIIEAQTEQTTDLTTKSLSSTYLKKYVMPKD
Sbjct:    1 MEVNINNTTSDLNPINYFTNKYSFYSYFYPSESDEGLLPFAKQFQNSVDEKTYFSSTEDPSKPMVTNFTKTDRRLKMIENKCGVEIKIGGIEDKLMRGLPRRKVTIYSQKHEKIAAALSCIENAIPELLEKALFTEPLNCKTHNWPTANGLFIRQLRKSKFFHKRALNCPLGKSSWSNVIDPKKIFPFKTASFSLRTSVLHNTNKITSKNNISPINEDNDIIIEAQTEQTTDLTTKSLSSTYLKKYVMPKD 251          
BLAST of SMED30003180 vs. Planmine SMEST
Match: SMESG000014661.1 (SMESG000014661.1)

HSP 1 Score: 83.1889 bits (204), Expect = 1.644e-17
Identity = 54/154 (35.06%), Postives = 83/154 (53.90%), Query Frame = -2
Query: 2485 DEGLLPFAKQFQNSVDEKTYFSSTEDPSKPMVTNFTKTDRRLKMIENXXXXXXXXXXXXXKLIRGLPRRKVTIYSQKHEKIAAALSCIENAIPELLEKALFTEPLNCKTHNWPTANGLFIRQLRKSKFFHKRALNCPLGKSSWSNVIDPKKIFP 2946
            D GL PF K     ++E  Y +S ++ S+    N  + DRR+K IE K   +IKI  ++ + I+GLP R++TI  +  ++IA AL+  ++ IP++L  A+F   LN  T NWP      +R L K+K    R+       + W N I   +IFP
Sbjct:   60 DVGLTPFVKHMAQKLEEDEYKNSFDEFSE--YPNEIRQDRRIKSIEVKSNCQIKISNLDHRFIKGLPMRRITISGKSDDQIARALTIFQDMIPDILRNAVFMSTLNSTTTNWPVPGKFIVRPLIKTK-SSTRSTQSNNKPAPWQNRIQKNRIFP 210          
BLAST of SMED30003180 vs. Planmine SMEST
Match: SMESG000063608.1 (SMESG000063608.1)

HSP 1 Score: 69.707 bits (169), Expect = 9.825e-12
Identity = 46/142 (32.39%), Postives = 76/142 (53.52%), Query Frame = -2
Query: 2410 DRRLKMIENXXXXXXXXXXXXXKLIRGLPRRKVTIYSQKHEKIAAALSCIENAIPELLEKALFTEPL-NCKTHNWPTANGLFIRQLRKSKFFHKRALNCPLGKSSWSNVIDPKKIFPFKTASFSLRTSVLHNTNKITSKNNI 2832
            DRRL+MIEN C  +I +  +    I+GLPRR V IYS  +E +A ALS +E  +PE+++ A+  E L +  +  W ++  L  R ++  +  H        G S+W++ +D K+ FP     F     ++  T+K +   N+
Sbjct:  378 DRRLEMIENHCKCKIVLEPLNMDFIKGLPRRPVAIYSMNYEDVAKALSILEEVMPEIMKTAILKERLPSTYSKKW-SSESLIHRPVKLYRSNH--------GSSTWNDRLDTKRRFPSTKKLFKKTVHLMPQTSKKSVFGNV 510          
The following BLAST results are available for this feature:
BLAST of SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 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 SMED30003180 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000013216.11.484e-13899.20SMESG000013216.1[more]
SMESG000014661.11.644e-1735.06SMESG000014661.1[more]
SMESG000063608.19.825e-1232.39SMESG000063608.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003180 ID=SMED30003180|Name=SMED30003180|organism=Schmidtea mediterranea sexual|type=transcript|length=3460bp
GCTTTAAAACCAAAATACCAAACGAAAAGTATGTGTCATGACTGAAAAAT
AGGCCGGAATTACAATGTTGCCTAGAACCACTTTAGCTTTAGTTCGCCAC
TGAGAATAATAGATACGAATTTATTATTTTCAATGATATCAGGATTTTAC
TTGATTAAAAGAAACAATTTATATTTATATTAGGTAATATATGTAAAGTT
CTGGGAATTACTAAAAGTATTATTAATTATTAATTTGAAGTCGTTTTAAT
TTTTTAGACAATATAATGATAATTACAGGATTTTATTCCAAGAACTACTA
TATTATTAGCAAATATTTTGGCACATAAAGAATTGTGCCTTACATATTTT
AAAGCTAGAAATATCTTTAAAATCTTTCTTTTAATAAAACATAAAGTTCA
TCAGTAAAACAATATATATTTTTTTATAAATGGTTTAATCAAAAATAACT
TACGTATTTCTCAAGTGTATTGACGCTACCAAAACCCTTGCTCATCAAAA
ATTCTTGTGAAAAAATGGTTGAGAAACTCTGGTAAAATAGTGCTGGAAAA
CTTTATTTAATTAAAATTAATACAAACAGATAAATTAAAATTAAAATTCA
GTAAAATATGTTGCGTTAGAGAACCTCGATAACATTAAGAAACACTTTCT
GAGTTTCTAACGGCTTTATCATTGGCAATACTTGCAAATTTTGTCAAGTT
TTCTTCATTTTATATGTTTCTTTGACATCAATCATCTGCATCAACAAGCC
ATTTCAGCTATTTTCTTCGATCTTCAATAAGAACATTACTAAATCAATAA
CCCAAATTTTTCTGTTGAGTCCCAACTTGACAAGCCACAATTACGCCTGT
CAAGTCGGCAATTTCATTTCTTAAAAGAAATGATAGATGTCTTCAGTAAA
ATTTTAATTACTTAACATGTATTTTTGTAATTTCATTGTCTGGAAACTTC
CCACTAATTAAAAATTATTATATTCGTCTTTAACTTTTCATTCGTTATCT
GCTCATAAAATCTCAGAGAAAGTATTTTAAAATTCTACATTAAATTTTGT
AGATATATCATATTATTTCTGCAATTCTTTAATGATGTTAGCATAAAACT
GTTTTTAAATAAACTTTATTATTTATTATAAGTTTTATTTGTAAAATTTT
CCCAATTAAAAAAGTCGAGCTTAGAAAAGGTTTAGGAAATCCCGATTTAC
ATGTTTGTTTTATAACAAATTTTTTTTTTCAATAGTTTAGTTCTATTATC
TGAGCTAATTCAGATTTCAATGTTGCCCTTTTAGTTTTATCCTTAGTAAT
TAATTTTGAATCAAAGGTTATTTATCATTATCATGTTTACATCTAAATTT
TTATTTTAATCTGTCCTTAACTGTATTATTTCAGATATCTTTCAGTGATT
CATCCTACAGTACTGGTGCCAGCATATCGACTTCAACTGCTAATAGGTTT
TTTTTCGAAAAAAAACCAGAGAGCAAGGTGAAACGTTGCCTACACGTTAC
CACAAACACAACAGCATAATATTGATTATGCTGAACCTTAATTATATTGG
AATTGGATTATAATTTTGCATGAACTCTGTACTCAGCCGATATCATAGAG
CCTCATTGATATAGCTCCCAATAAGTGTAATGCTATTTAGATAGAGATAA
TGATAAAGCACTTCAACAATCAGCTCTCTCTATAGGGTTTGAATATAATC
CTTTATTCAAGAGCACTCCAATTGGTGCTACTCCAACATTACACATATCT
AGTATGAAAACAGCTGCTTCTATGAAAAACCCACAACCTTAGTAAAGCAA
TCTAAAAGAGTCAACTGATACTGTAATGTAGAGTTTTCGGGAGTGATTTC
AACAATTTTTTATTTATAATTTTGATTACCAGGATATAAGTTTCAACGTG
TGCTGCTTGAAACCAACAAAACATCTGGTTTGTGTTTTTTTTTCAATTAT
GAATTTAAAAACAACAGCAAAAATACAATAAAACAGGCACATGAATCCGT
TTTTCACTATCGATTTTTATTCAATTAACTTCATTGATGTTCATTGTGAA
AGTTTATTAAAAATTAAATTCAACAATAATATTTTCAAGAGCTCGACCAA
GTTTCAGCTGTTGTCGATGACAGCTGATAGATATTAATAAATTCATTCAT
CTTCAGTTTCCGATCCAAACCCGACTAGGCTCATTGGTGAGAGCTGAAGT
GAATTCATCTGCAGCCTGGTACCTAGTGAGCGAACGCATAACGAAGCCGC
TGATGGTTTGTTATTATTACTAATATTATTATTAATATTATTATCTTTAG
GCATTACGTACTTTTTCAAGTATGTACTACTAAGAGACTTCGTGGTTAAG
TCCGTAGTTTGTTCTGTTTGAGCTTCTATTATAATGTCGTTATCCTCATT
AATGGGAGAAATATTATTTTTTGAAGTGATTTTATTCGTATTGTGAAGAA
CTGACGTTCGCAAACTAAAAGATGCGGTTTTAAATGGGAAAATCTTCTTG
GGATCAATTACGTTACTCCAAGACGATTTGCCAAGAGGACAATTAAGAGC
TCTTTTATGAAAGAACTTTGATTTTCTTAACTGTCTAATAAACAAACCGT
TGGCTGTTGGCCAGTTATGAGTTTTGCAATTCAAAGGCTCTGTGAATAAT
GCCTTTTCTAATAGTTCTGGAATTGCATTTTCGATGCAAGATAAAGCCGC
TGCGATCTTTTCGTGTTTTTGCGAATAAATTGTAACTTTTCTTCTTGGTA
GGCCTCTGATTAATTTTTCCTCTATGCCACCGATTTTTATTTCTACCCCA
CATTTGTTTTCAATCATTTTCAATCGTCTATCGGTTTTGGTAAAATTTGT
CACCATTGGTTTTGATGGGTCTTCAGTACTTGAAAAATAGGTCTTCTCGT
CAACAGAATTCTGAAACTGCTTTGCGAACGGAAGTAAACCTTCGTCAGAT
TCTGAGGGATAGAAATAACTGTAAAATGAATATTTGTTTGTAAAATAATT
GATAGGATTCAAATCGGATGTTGTGTTATTAATATTAACTTCCATTTCAT
TTGTATTTTTTGTTATCATTTCAACGCACAGGGTTTCTTGTTTATTGAAT
TTGGTTTTCTCTTTAAACTTATCATGGACCTTTGAAAGATCATATTTCCG
GTTGATAATGCTTCGATATTTGCTGGAACGATAATAAATATTATTACTAT
TAGATTCATTTGTCTCATTTAGAATAGCACAATTAGAACTCCTCTGGGTC
GCGATTTGGGAATCCACACTTGATAGAGACTCACAGCTCAGATTTTCCTC
TGAAGGCGTTTGTTTCTTTTTTCTCTTTAATGTCAGAGACTCATTCGAGT
GAGATTTTATTAAGTGAATAAGTTTAACCTTGATAGTCATTTTCAAACAT
CCAATTAATGATTTTTAATAATTGTTTTTTATTCAATTAAACATTTAAAC
TAGGTCTCCT
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protein sequence of SMED30003180-orf-1

>SMED30003180-orf-1 ID=SMED30003180-orf-1|Name=SMED30003180-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=416bp
MTIKVKLIHLIKSHSNESLTLKRKKKQTPSEENLSCESLSSVDSQIATQR
SSNCAILNETNESNSNNIYYRSSKYRSIINRKYDLSKVHDKFKEKTKFNK
QETLCVEMITKNTNEMEVNINNTTSDLNPINYFTNKYSFYSYFYPSESDE
GLLPFAKQFQNSVDEKTYFSSTEDPSKPMVTNFTKTDRRLKMIENKCGVE
IKIGGIEEKLIRGLPRRKVTIYSQKHEKIAAALSCIENAIPELLEKALFT
EPLNCKTHNWPTANGLFIRQLRKSKFFHKRALNCPLGKSSWSNVIDPKKI
FPFKTASFSLRTSVLHNTNKITSKNNISPINEDNDIIIEAQTEQTTDLTT
KSLSSTYLKKYVMPKDNNINNNISNNNKPSAASLCVRSLGTRLQMNSLQL
SPMSLVGFGSETEDE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium