SMED30011205

Overview
NameSMED30011205
Smed IDSMED30011205
Length (bp)1626
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30011205 (SMED30011205) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011205 (SMED30011205) 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.
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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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Anatomical Expression

PAGE et. al., 2020




SMED30011205

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30011205SMESG000056922.1 SmedASXL_015956SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
parenchymal cellSMED30011205SMESG000056922.1 dd_Smed_v4_11352_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermal cellSMED30011205SMESG000056922.1 dd_Smed_v4_11352_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30011205SMESG000056922.1 dd_Smed_v6_11352_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30011205SMESG000056922.1 dd_Smed_v4_11352_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30011205SMESG000056922.1 dd_Smed_v4_11352_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30011205SMESG000056922.1 dd_Smed_v4_11352_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
Homology
BLAST of SMED30011205 vs. Planmine SMEST
Match: SMESG000056922.1 (SMESG000056922.1)

HSP 1 Score: 531.946 bits (1369), Expect = 0.000e+0
Identity = 275/282 (97.52%), Postives = 278/282 (98.58%), Query Frame = 3
Query:  144 LFEGDITCVLIKQREKKIRDINVSINEKNNKKNDRPKTIDCQYKTYLHDTFESINEKNNAKNDRPKTTDWQYKNYLHDTFKDILSEIEXXXXXXXXXXXXYETLGRLYGSLELEYINFNESKTVTFEDLKRYFLIFDKLWQPSILQTIKENDKFEEIEKLAINCWCVSVNLASLYLFHSLPENNLADDVIKIIIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRICFSQNLSLSIKIASGIILSFKFPSNPIMCDVFRDLECLKL 989
            +FEGDI CVLIKQREKKIRDINVS+NEKNNKKNDRPKTIDCQYKTYLHDTFESINEKNNAKNDRPKTTDWQYKNYLHDTFKDILSEIEKDDFMKNDKNKKYETLGRLYGSLELEYINFNESKTVTFEDLKRYFLIFDKLWQPSILQTIKENDKFEEI KLAINCWCVSVNLASLYLFHSLPENNLADDVIKIIIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRICFSQNLSLSIKIASGIILSFKFPSNPIMCDVFRDLE  K+
Sbjct:    1 MFEGDIMCVLIKQREKKIRDINVSMNEKNNKKNDRPKTIDCQYKTYLHDTFESINEKNNAKNDRPKTTDWQYKNYLHDTFKDILSEIEKDDFMKNDKNKKYETLGRLYGSLELEYINFNESKTVTFEDLKRYFLIFDKLWQPSILQTIKENDKFEEIVKLAINCWCVSVNLASLYLFHSLPENNLADDVIKIIIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRICFSQNLSLSIKIASGIILSFKFPSNPIMCDVFRDLEYFKI 282          
BLAST of SMED30011205 vs. Planmine SMEST
Match: SMESG000056922.1 (SMESG000056922.1)

HSP 1 Score: 520.39 bits (1339), Expect = 0.000e+0
Identity = 270/275 (98.18%), Postives = 272/275 (98.91%), Query Frame = 3
Query:  165 CVLIKQREKKIRDINVSINEKNNKKNDRPKTIDCQYKTYLHDTFESINEKNNAKNDRPKTTDWQYKNYLHDTFKDILSEIEXXXXXXXXXXXXYETLGRLYGSLELEYINFNESKTVTFEDLKRYFLIFDKLWQPSILQTIKENDKFEEIEKLAINCWCVSVNLASLYLFHSLPENNLADDVIKIIIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRICFSQNLSLSIKIASGIILSFKFPSNPIMCDVFRDLECLKL 989
            CVLIKQREKKIRDINVS+NEKNNKKNDRPKTIDCQYKTYLHDTFESINEKNNAKNDRPKTTDWQYKNYLHDTFKDILSEIEKDDFMKNDKNKKYETLGRLYGSLELEYINFNESKTVTFEDLKRYFLIFDKLWQPSILQTIKENDKFEEI KLAINCWCVSVNLASLYLFHSLPENNLADDVIKIIIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRICFSQNLSLSIKIASGIILSFKFPSNPIMCDVFRDLE  K+
Sbjct:    2 CVLIKQREKKIRDINVSMNEKNNKKNDRPKTIDCQYKTYLHDTFESINEKNNAKNDRPKTTDWQYKNYLHDTFKDILSEIEKDDFMKNDKNKKYETLGRLYGSLELEYINFNESKTVTFEDLKRYFLIFDKLWQPSILQTIKENDKFEEIVKLAINCWCVSVNLASLYLFHSLPENNLADDVIKIIIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRICFSQNLSLSIKIASGIILSFKFPSNPIMCDVFRDLEYFKI 276          
BLAST of SMED30011205 vs. Planmine SMEST
Match: SMESG000056914.1 (SMESG000056914.1)

HSP 1 Score: 56.9954 bits (136), Expect = 1.026e-8
Identity = 32/111 (28.83%), Postives = 57/111 (51.35%), Query Frame = 3
Query:  537 YFLIFDKLWQPSILQTIKENDKFEEIEKLAINCWCVSVNLASLYLFHSLPENNLADDVIKIIIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRI 869
            +   F+   Q  IL  IK    F   EK A+NC  +S++  ++ +       +++  +I  +I ++  +  + +SN ++RR+VE+ LYCLCN    ++  N   LEK   I
Sbjct:  113 FLKFFNNPLQNEILNKIKSKTDFNNYEKTALNCISISISTINMMM------KDVSPSIILHVISFVSNYEPYSESNAISRRIVEMSLYCLCNY---FEQKNNSTLEKEFLI 214          
The following BLAST results are available for this feature:
BLAST of SMED30011205 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 SMED30011205 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 SMED30011205 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 SMED30011205 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 SMED30011205 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 SMED30011205 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 SMED30011205 vs. UniProt
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 SMED30011205 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 SMED30011205 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 SMED30011205 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 SMED30011205 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 SMED30011205 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 SMED30011205 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 SMED30011205 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000056922.10.000e+097.52SMESG000056922.1[more]
SMESG000056922.10.000e+098.18SMESG000056922.1[more]
SMESG000056914.11.026e-828.83SMESG000056914.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011205 ID=SMED30011205|Name=SMED30011205|organism=Schmidtea mediterranea sexual|type=transcript|length=1626bp
ATCAGCGTTTCGATTCTCAGATCACCAAAGCAATCTTACAAAACTTTGGT
GTTGATTTCATATATTTAAATTTATATGAATCTTAACTTCGCCTGACAGC
AAGACTTTTCCTTCACTCAATGCACCAACTGCAACAAGACAGATTGTTCG
AAGGAGATATTACGTGTGTCTTAATAAAACAAAGAGAAAAAAAGATTCGA
GATATCAATGTGAGTATCAATGAGAAAAATAATAAAAAGAATGACAGACC
AAAGACAATTGATTGTCAATACAAAACTTACTTACACGACACTTTCGAAA
GTATTAATGAGAAAAATAATGCAAAGAACGACAGACCAAAGACAACTGAT
TGGCAATACAAAAACTACTTGCACGACACTTTCAAAGATATTCTATCAGA
AATAGAAAAAGATGACTTTATGAAAAATGATAAAAATAAAAAGTATGAAA
CCTTAGGGAGACTCTACGGATCTCTTGAATTGGAATATATAAATTTTAAT
GAAAGTAAAACTGTTACATTTGAAGATTTAAAAAGATATTTCTTGATATT
TGATAAATTATGGCAGCCCTCCATTCTACAAACCATTAAGGAGAATGATA
AGTTTGAGGAAATTGAGAAATTAGCTATTAATTGTTGGTGCGTAAGCGTC
AATCTAGCGAGTCTCTATTTATTCCACTCGCTGCCCGAGAATAATTTAGC
TGATGATGTAATTAAGATCATAATCGGCTATTTAGATGCGTTCCACTCGC
ACGTCCAGTCCAATGGCGTGGCCAGGCGATTGGTGGAAGTCGTTCTATAT
TGCCTTTGCAATGCCTGTAAATCATATAAATTGTCCAATGAAGAAATTCT
TGAGAAATCATTGCGGATATGTTTTTCGCAAAACCTTTCATTATCAATCA
AAATCGCGTCCGGAATTATTTTATCATTCAAGTTTCCCAGTAATCCAATC
ATGTGTGACGTTTTCCGTGATCTTGAATGTTTGAAACTGGAAGATGAAAC
TTATCTTGGAATTGACAAACTCTTGATAACTGAAGCCTTGAATAAATTGC
GAAAAAGATTTTAAAATTTCATTTTTATTAAGTTAAGTTTAAATATATTT
TCAGTGTTTTTAAGTTGGTTAATATCGCCGCTTTCATTGCAGGAGAGAAT
TCTTTCCAGGCACCAAGGCTTGAATTCATCCTGCTAAGTAGCAATTCAAT
TAGTTACAACTGATACCTTTACGTCTGCGATTCAGAGTTTGAATCCTGAG
GAAGACGAATTTCAAGATTTCAAGGTACACTACTCTGATCCCCACCCTCT
CGAAAATCAGATGTTAAAATGGTAAATGATATTAAGATGTGATTTGAACA
ATTTGGCTGTCACATAAAATAATCATTTCAACCATTTTCTGCTGTCAGTC
GGTCTAATGCAGTTCACGGATAACTCCAGCCACCCGTCAACCATTTGATT
TCATTAAGTTTCCACTTACCACCGACAGATGCCATCGCAAACTTTAGTTA
TATTAGGTTGATACGTAATTATCTGGCGTTTTCTAGACATTTTTTGTTAT
TAGAAATGTCTTCGAAATACATTGAAAACATGTTCATTAGGTCATTATAG
ATCATTTAAAAACCCATGCTTCCATA
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protein sequence of SMED30011205-orf-1

>SMED30011205-orf-1 ID=SMED30011205-orf-1|Name=SMED30011205-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=315bp
MHQLQQDRLFEGDITCVLIKQREKKIRDINVSINEKNNKKNDRPKTIDCQ
YKTYLHDTFESINEKNNAKNDRPKTTDWQYKNYLHDTFKDILSEIEKDDF
MKNDKNKKYETLGRLYGSLELEYINFNESKTVTFEDLKRYFLIFDKLWQP
SILQTIKENDKFEEIEKLAINCWCVSVNLASLYLFHSLPENNLADDVIKI
IIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRI
CFSQNLSLSIKIASGIILSFKFPSNPIMCDVFRDLECLKLEDETYLGIDK
LLITEALNKLRKRF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000096ventral epidermis
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell