SMED30008179

Overview
NameSMED30008179
Smed IDSMED30008179
Length (bp)1567
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 SMED30008179 (SMED30008179) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008179 (SMED30008179) 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 SMED30008179 (SMED30008179) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008179 (SMED30008179) 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



SMED30008179

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30008179SMESG000006319.1 Contig13871newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008179SMESG000006319.1 Contig13871uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
reproductive organSMED30008179SMESG000006319.1 Contig13871newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30008179SMESG000006319.1 Contig13871uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30008179 vs. Planmine SMEST
Match: SMESG000041615.1 (SMESG000041615.1)

HSP 1 Score: 338.576 bits (867), Expect = 6.116e-115
Identity = 164/184 (89.13%), Postives = 174/184 (94.57%), Query Frame = 3 
Query:  924 FCD-MNSRQILNNEESSARVLNEDAVTNLDVQTEETSGALKWVPTGIAEEWRRARQLLWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQRDGQHPAREILEHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRILETYSEAPPPKHGPVRNTRRPVFVVSGCSAK*WLEKSLEQL 1472
            +C+ MNS+  LNNEE+SARVLNEDAV NLD+QT+ETSGALKWVP GIAEEWR+ARQ+LWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQ+  QHPAREILEHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDV AGRILETYSEAPPPKHGPVRNTR+PVFV SGCSAK WLEKSLEQL
Sbjct:   26 YCNNMNSQPTLNNEETSARVLNEDAVMNLDLQTKETSGALKWVPAGIAEEWRQARQILWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQKGEQHPAREILEHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVTAGRILETYSEAPPPKHGPVRNTRQPVFVASGCSAKEWLEKSLEQL 209

HSP 2 Score: 47.3654 bits (111), Expect = 8.207e-6
Identity = 20/25 (80.00%), Postives = 22/25 (88.00%), Query Frame = 2 
Query:  848 YETHPLCRFDNSALTITIQTEILDF 922
            YETHPLCRFD S  TITIQTEIL++
Sbjct:    2 YETHPLCRFDKSTSTITIQTEILEY 26
[Close]
BLAST of SMED30008179 vs. Planmine SMEST
Match: SMESG000037791.1 (SMESG000037791.1)

HSP 1 Score: 296.59 bits (758), Expect = 2.068e-98
Identity = 150/209 (71.77%), Postives = 169/209 (80.86%), Query Frame = 3 
Query:  864 SVDLIIVHSQSPFKQKFWI----FFCDMNSRQILNNEESSARVLNEDAVTNLD--VQTEETSGALKWVPTGIAEEWRRARQLLWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQRDGQHPAREILEHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRILETYSEAPPPKHGPVRNTRRPVFVVSGCSAK*WLEKSLEQL 1472
            +V ++   S    + KF+     F   +     L+   S +++  + ++ N D  + + ETS ALKWVP GIAEEWR+AR+LLWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQ+D QHPAREILEHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDV+AGRILETYSEAPPPKHGPVRNTRRPVFVVS CSAK WLEKSLEQL
Sbjct:    5 TVIMLSCSSTYSLQDKFYFSLERFTIMIFGTMTLDTTSSHSKL--QSSINNYDPPLSSYETSEALKWVPAGIAEEWRQARRLLWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQKDEQHPAREILEHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVSAGRILETYSEAPPPKHGPVRNTRRPVFVVSRCSAKEWLEKSLEQL 211
[Close]
BLAST of SMED30008179 vs. Planmine SMEST
Match: SMESG000061667.1 (SMESG000061667.1)

HSP 1 Score: 278.485 bits (711), Expect = 8.509e-92
Identity = 135/179 (75.42%), Postives = 151/179 (84.36%), Query Frame = 3 
Query:  933 MNSRQILNNEESSARVLNEDAVTNLDVQTEETSGALKWVPTGIAEEWRRARQLLWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQRDGQHPAREILEHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRILETYSEAPPPKHGPVRNTRRPVFVVSGCSAK*WLEKSLEQ 1469
            MN R ILN EE+SA++ N     + D++ + TSGALKWVP G+ EEWR+AR+LLWRAKGYE+PSPRGPSQTI QMLGMDQQ PVA E  D QHPAREIL HAR LLDRLEAHQ+QVDLHVVRVRQYLANVEDDVAAGRIL+TYSE PPP H PVRNTRRPVFV SG +A+ WL+KSLEQ
Sbjct:    1 MNRRPILNAEETSAKLCNRGTAMDFDLRVKNTSGALKWVPAGMTEEWRQARRLLWRAKGYEKPSPRGPSQTICQMLGMDQQSPVAAEYNDEQHPAREILAHARGLLDRLEAHQKQVDLHVVRVRQYLANVEDDVAAGRILDTYSEVPPPNHRPVRNTRRPVFVTSGYTAEEWLQKSLEQ 179
[Close]
BLAST of SMED30008179 vs. Planmine SMEST
Match: SMESG000031496.1 (SMESG000031496.1)

HSP 1 Score: 273.478 bits (698), Expect = 8.028e-90
Identity = 139/180 (77.22%), Postives = 165/180 (91.67%), Query Frame = 3 
Query:  933 MNSRQILNNEESSARVLNEDAVTNLDVQTEETSGALKWVPTGIAEEWRRARQLLWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQRDGQHPAREILEHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRILETYSEAPPPKHGPVRNTRRPVFVVSGCSAK*WLEKSLEQL 1472
            MNS+++ N++E+SA++ NE AV +LD++T++TSGAL WVPTGIA+EWR+AR+LL RAKGYE+PSPRGPSQTIGQMLG+DQ+LP+ D+++D Q+PAREIL H RELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRI+ETYSEAPPP HGPV NTRRPVFVVSG SA+ WL KSLEQL
Sbjct:    1 MNSQRVWNDKETSAKLPNEGAVMDLDLRTKDTSGALMWVPTGIADEWRQARRLLRRAKGYEKPSPRGPSQTIGQMLGIDQRLPLTDDRKDEQYPAREILRHVRELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRIMETYSEAPPPNHGPVLNTRRPVFVVSGYSAEEWLRKSLEQL 180
[Close]
BLAST of SMED30008179 vs. Planmine SMEST
Match: SMESG000025478.1 (SMESG000025478.1)

HSP 1 Score: 265.774 bits (678), Expect = 2.006e-87
Identity = 130/142 (91.55%), Postives = 137/142 (96.48%), Query Frame = 3 
Query: 1047 VPTGIAEEWRRARQLLWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQRDGQHPAREILEHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRILETYSEAPPPKHGPVRNTRRPVFVVSGCSAK*WLEKSLEQL 1472
            VPTGIAEEWR+AR+LLWR+KGYEEPSPRGP QTIGQMLGMDQ+LPVADE++D Q+PAREIL HARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRILETYSEAPPPKHGPVRNT RPVFVVSGCSAK WLEKSLEQL
Sbjct:    3 VPTGIAEEWRQARRLLWRSKGYEEPSPRGPRQTIGQMLGMDQRLPVADERKDEQYPAREILGHARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRILETYSEAPPPKHGPVRNTGRPVFVVSGCSAKEWLEKSLEQL 144
The following BLAST results are available for this feature:
BLAST of SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 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 SMED30008179 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000041615.16.116e-11589.13SMESG000041615.1[more]
SMESG000037791.12.068e-9871.77SMESG000037791.1[more]
SMESG000061667.18.509e-9275.42SMESG000061667.1[more]
SMESG000031496.18.028e-9077.22SMESG000031496.1[more]
SMESG000025478.12.006e-8791.55SMESG000025478.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008179 ID=SMED30008179|Name=SMED30008179|organism=Schmidtea mediterranea sexual|type=transcript|length=1567bp
CCAAAATCATCATAATTAATTACAACCTACTGATCGCCACCTAGGGAGCA
TGATCTGATCATAGAAAGTTTGAATTAAATCAATTTTAATAGAAATAAAG
TACAGCCAAACCCATCAGAACTAAAATCCGTTATAAAAATTCACGAAAAG
TTCCGGACGAATAATAAGATTTTTGATCGACTCCCACAGGTTGAAAACTA
AATAATTTTTTTTATTAAAATTCCTAAAGGTACTAAGAATATAATTATGA
AACCATACCCATACTTAATAAAAATTCCTGGTACGCCCCAAACGATTAAC
GAATATAGTTTCCAAATCTTCACCGTTAAACAACAAAAAACACCCCTAAA
AATCTGAATAGAAATGTTATAAAGTTGAATTCCATTTATCACCTGTACGA
CCAAGAAGACAGAGATTCATCAATTTTCATAACCCAGAACTTGACTATCC
CGATTAAGATTCTCGTACGCCAACTCGAATTTAGAAATAGCGTTAAAATT
TTCCACAACTAATTCGCTAAAAAGGATTAAAAAATCAATGACTAAAAATA
TACGTATTACTAGATACAAATGTTGATGATTTCGACCGTAAATCTGCACC
CAAATCCCTTATTCCAACAAGGCGAATCTCTAAATAAAATCAATAAAAAT
CAAACGTAAATTACAATCAACCAACCGAGTCGTCAATCACCCTATCAAAC
TATTACAATAATTAACATAAACATTCATAGTTCACTGCAATCCACATTGG
TTTTCAATTTTTCACTGAATAAATAAGTTCACCGGAAATCTATCGATTAT
TTACCACTACCAGGCACAGTGTGTCAACGATTACAACAGTAAGCAGATAC
GAAACACACCCACTCTGTCGATTTGATAATAGTGCACTCACAATCACCAT
TCAAACAGAAATTTTGGATTTTTTTTTGCGACATGAATTCTCGACAAATT
TTGAATAATGAAGAGTCCTCGGCTAGGGTACTCAACGAAGATGCAGTAAC
AAATCTGGATGTACAAACGGAGGAAACATCAGGAGCTCTCAAGTGGGTTC
CCACTGGCATTGCAGAAGAATGGAGACGGGCTCGGCAACTACTATGGCGA
GCAAAGGGCTACGAGGAGCCATCTCCGAGAGGACCCAGTCAAACAATTGG
CCAGATGTTGGGAATGGACCAGCAGTTACCAGTGGCCGATGAACAAAGAG
ACGGACAGCACCCAGCCCGCGAAATTCTAGAACATGCTCGCGAACTACTC
GACCGACTAGAAGCACACCAAAGGCAAGTAGATCTCCACGTGGTCCGGGT
CAGGCAATACCTGGCCAACGTGGAAGATGACGTCGCTGCGGGGAGAATCC
TGGAAACCTATAGTGAGGCGCCGCCACCCAAGCACGGACCGGTGCGGAAT
ACAAGACGGCCCGTATTCGTAGTCTCGGGTTGCTCGGCAAAGTAATGGTT
GGAAAAATCCCTAGAACAACTATGATCATCCGGACTGGCGATTGTAAATT
TTTGATTAACATGGATATAATATAAATAATTGCCGGAGTTTTCATTTTGC
TTGTTTTGCTTTCCTAA
back to top

protein sequence of SMED30008179-orf-1

>SMED30008179-orf-1 ID=SMED30008179-orf-1|Name=SMED30008179-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=171bp
MNSRQILNNEESSARVLNEDAVTNLDVQTEETSGALKWVPTGIAEEWRRA
RQLLWRAKGYEEPSPRGPSQTIGQMLGMDQQLPVADEQRDGQHPAREILE
HARELLDRLEAHQRQVDLHVVRVRQYLANVEDDVAAGRILETYSEAPPPK
HGPVRNTRRPVFVVSGCSAK*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ