SMED30016497

Overview
NameSMED30016497
Smed IDSMED30016497
Length (bp)504
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 SMED30016497 (SMED30016497) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016497 (SMED30016497) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 SMED30016497 (SMED30016497) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016497 (SMED30016497) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top


 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30016497

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30016497SMESG000000587.1 dd_Smed_v4_12110_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30016497SMESG000000587.1 dd_Smed_v4_12110_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
SMED30016497 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001646:48113..48605 -2003
v31.001646:48607..49125 -1413
Homology
BLAST of SMED30016497 vs. Planmine SMEST
Match: SMESG000000587.1 (SMESG000000587.1)

HSP 1 Score: 233.802 bits (595), Expect = 9.939e-75
Identity = 128/154 (83.12%), Postives = 137/154 (88.96%), Query Frame = 2
Query:    2 NEHCTNETRKSQEYLPKSDRKKLFLINLDKIRTFFSKIILNKTKTDVDESDVGKTQIEAXXXXXXXXXIFLQRELSKSLPAIAEINDTDQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTDNKATNRGNQNTVGVEHENNN 463
            NEHCTNETRKSQEYLPKSDRKKLFLINLDKIRTFFSKIILNKTKTDVDESDVGKTQIEAKSKKQKFKKIFLQRELSKSLPAIAEINDTDQYDEIYSNK  E+ N + +K NE R  YRD PFL N EIY+EVTD KATN GN++T+ V + N+N
Sbjct:  115 NEHCTNETRKSQEYLPKSDRKKLFLINLDKIRTFFSKIILNKTKTDVDESDVGKTQIEAKSKKQKFKKIFLQRELSKSLPAIAEINDTDQYDEIYSNKMKEKANVLIIKMNETRNFYRDRPFLGNHEIYAEVTDYKATNSGNESTIRVGYNNSN 268          

HSP 2 Score: 189.889 bits (481), Expect = 6.220e-58
Identity = 101/127 (79.53%), Postives = 102/127 (80.31%), Query Frame = 2
Query:  122 NKTKTDVDESDVGKTQIEAXXXXXXXXXIFLQRELSKSLPAIAEINDTDQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTDNKATNRGNQNTVGVEHENNNIKVDRINTTKIRK 502
            NKTK DVD SD  K Q                 +LSKSL  IAEIND DQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTDNKATNRGNQNTVGVEHENNNIKVDRINTTKIRK
Sbjct:    4 NKTKKDVDISDKAKRQ-----------------KLSKSLSNIAEINDIDQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTDNKATNRGNQNTVGVEHENNNIKVDRINTTKIRK 113          
BLAST of SMED30016497 vs. Planmine SMEST
Match: SMESG000000587.1 (SMESG000000587.1)

HSP 1 Score: 233.802 bits (595), Expect = 1.338e-74
Identity = 128/154 (83.12%), Postives = 137/154 (88.96%), Query Frame = 2
Query:    2 NEHCTNETRKSQEYLPKSDRKKLFLINLDKIRTFFSKIILNKTKTDVDESDVGKTQIEAXXXXXXXXXIFLQRELSKSLPAIAEINDTDQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTDNKATNRGNQNTVGVEHENNN 463
            NEHCTNETRKSQEYLPKSDRKKLFLINLDKIRTFFSKIILNKTKTDVDESDVGKTQIEAKSKKQKFKKIFLQRELSKSLPAIAEINDTDQYDEIYSNK  E+ N + +K NE R  YRD PFL N EIY+EVTD KATN GN++T+ V + N+N
Sbjct:  137 NEHCTNETRKSQEYLPKSDRKKLFLINLDKIRTFFSKIILNKTKTDVDESDVGKTQIEAKSKKQKFKKIFLQRELSKSLPAIAEINDTDQYDEIYSNKMKEKANVLIIKMNETRNFYRDRPFLGNHEIYAEVTDYKATNSGNESTIRVGYNNSN 290          

HSP 2 Score: 199.904 bits (507), Expect = 1.565e-61
Identity = 108/142 (76.06%), Postives = 110/142 (77.46%), Query Frame = 2
Query:   77 INLDKIRTFFSKIILNKTKTDVDESDVGKTQIEAXXXXXXXXXIFLQRELSKSLPAIAEINDTDQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTDNKATNRGNQNTVGVEHENNNIKVDRINTTKIRK 502
            I   KI  FFSK+  NKTK DVD SD  K Q                 +LSKSL  IAEIND DQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTDNKATNRGNQNTVGVEHENNNIKVDRINTTKIRK
Sbjct:   11 IKATKIMEFFSKMNANKTKKDVDISDKAKRQ-----------------KLSKSLSNIAEINDIDQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTDNKATNRGNQNTVGVEHENNNIKVDRINTTKIRK 135          
BLAST of SMED30016497 vs. Planmine SMEST
Match: SMESG000036117.1 (SMESG000036117.1)

HSP 1 Score: 130.568 bits (327), Expect = 1.793e-35
Identity = 71/109 (65.14%), Postives = 76/109 (69.72%), Query Frame = 2
Query:   77 INLDKIRTFFSKIILNKTKTDVDESDVGKTQIEAXXXXXXXXXIFLQRELSKSLPAIAEINDTDQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTD 403
            I   KIR FFS +  NKTK DVD+SD  K Q                 +LSKSLP IAEINDTDQYDEIYSNKRTERTNDIN KKNEPRIGYRDG FLDNQE+YSE  +
Sbjct:   11 IKATKIRAFFSIMNANKTKKDVDKSDKTKRQ-----------------KLSKSLPNIAEINDTDQYDEIYSNKRTERTNDINFKKNEPRIGYRDGSFLDNQEVYSEAIE 102          
BLAST of SMED30016497 vs. Planmine SMEST
Match: SMESG000000754.1 (SMESG000000754.1)

HSP 1 Score: 120.939 bits (302), Expect = 3.753e-32
Identity = 63/94 (67.02%), Postives = 69/94 (73.40%), Query Frame = 2
Query:  122 NKTKTDVDESDVGKTQIEAXXXXXXXXXIFLQRELSKSLPAIAEINDTDQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTD 403
            NKT+ DVD SD  K                 + +LSKSLP IAEIND DQYDEIYSNKRT+RTNDINLKKNEPRIGYRDGPFLDNQE+YSEV +
Sbjct:    4 NKTEKDVDISDKTK-----------------RHKLSKSLPNIAEINDADQYDEIYSNKRTQRTNDINLKKNEPRIGYRDGPFLDNQEVYSEVIE 80          
BLAST of SMED30016497 vs. Planmine SMEST
Match: SMESG000036117.1 (SMESG000036117.1)

HSP 1 Score: 120.553 bits (301), Expect = 6.945e-32
Identity = 64/94 (68.09%), Postives = 68/94 (72.34%), Query Frame = 2
Query:  122 NKTKTDVDESDVGKTQIEAXXXXXXXXXIFLQRELSKSLPAIAEINDTDQYDEIYSNKRTERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTD 403
            NKTK DVD+SD  K Q                 +LSKSLP IAEINDTDQYDEIYSNKRTERTNDIN KKNEPRIGYRDG FLDNQE+YSE  +
Sbjct:    4 NKTKKDVDKSDKTKRQ-----------------KLSKSLPNIAEINDTDQYDEIYSNKRTERTNDINFKKNEPRIGYRDGSFLDNQEVYSEAIE 80          
The following BLAST results are available for this feature:
BLAST of SMED30016497 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016497 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000000587.19.939e-7583.12SMESG000000587.1[more]
SMESG000000587.11.338e-7483.12SMESG000000587.1[more]
SMESG000036117.11.793e-3565.14SMESG000036117.1[more]
SMESG000000754.13.753e-3267.02SMESG000000754.1[more]
SMESG000036117.16.945e-3268.09SMESG000036117.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016497 ID=SMED30016497|Name=SMED30016497|organism=Schmidtea mediterranea sexual|type=transcript|length=504bp
CAATGAACATTGCACAAATGAAACAAGGAAATCTCAAGAATATCTTCCAA
AATCGGATCGTAAAAAATTGTTTTTAATTAATTTGGATAAGATAAGAACA
TTTTTTTCTAAAATTATTTTGAATAAAACGAAAACAGATGTTGATGAAAG
TGATGTTGGTAAAACTCAAATCGAGGCAAAATCGAAGAAACAAAAATTTA
AGAAAATATTTCTTCAAAGAGAACTCAGTAAATCTCTTCCAGCTATAGCA
GAAATAAATGACACGGACCAATATGATGAGATCTATTCGAATAAAAGGAC
AGAAAGAACAAATGATATTAATTTAAAAAAGAATGAACCAAGAATTGGTT
ATCGGGACGGGCCATTCTTGGATAACCAAGAAATTTACTCCGAGGTTACT
GATAATAAAGCGACAAACCGTGGGAATCAGAATACAGTCGGTGTTGAACA
TGAAAATAATAATATAAAAGTAGATAGAATAAATACAACAAAAATCAGAA
AAAG
back to top

protein sequence of SMED30016497-orf-1

>SMED30016497-orf-1 ID=SMED30016497-orf-1|Name=SMED30016497-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=167bp
NEHCTNETRKSQEYLPKSDRKKLFLINLDKIRTFFSKIILNKTKTDVDES
DVGKTQIEAKSKKQKFKKIFLQRELSKSLPAIAEINDTDQYDEIYSNKRT
ERTNDINLKKNEPRIGYRDGPFLDNQEIYSEVTDNKATNRGNQNTVGVEH
ENNNIKVDRINTTKIRK
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis