SMED30030925

Overview
NameSMED30030925
Smed IDSMED30030925
Length (bp)1925
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 SMED30030925 (SMED30030925) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030925 (SMED30030925) 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 SMED30030925 (SMED30030925) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030925 (SMED30030925) 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




SMED30030925

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
intestinal phagocyteSMED30030925 Contig3416GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30030925SMESG000038398.1 dd_Smed_v4_4195_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30030925SMESG000038398.1 dd_Smed_v4_4195_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30030925SMESG000038398.1 dd_Smed_v4_4195_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30030925SMESG000038398.1 dd_Smed_v4_4195_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30030925SMESG000038398.1 dd_Smed_v4_4195_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
testisSMED30030925SMESG000038398.1 GDAG01074296.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30030925 vs. Planmine SMEST
Match: SMESG000038398.1 (SMESG000038398.1)

HSP 1 Score: 985.712 bits (2547), Expect = 0.000e+0
Identity = 524/528 (99.24%), Postives = 527/528 (99.81%), Query Frame = 3
Query:  117 METTEYEEGYFKLKKSNEELVTLLNKVINDLKLLKISQKAEKEKNVALSTSNGNLSSEVIQLTRKCEKQLKTIGDLNNELDYLKSYSKAVEGVAENYCGQTISTQKKYDQLKRQSSIFFNNFQDQSLINIDLNDHESETESCDTPTPILEFEEIKKNHEEILDKEKQKYDILRTELNESQTEVIGLKSEIENANQRLEEKQQDNDKLNQEMDILIKSYSNLKDDHDKMMNYFAPFLRMKAENQELKRTSALLLNNVAGDEKIIEFLSMIEDLXXXXXXXXXXXXALELQISECEQSTVMLELSTVKSEVDDLARKLESLTKERDTLKHENRILLEQKGGFGIAXXXXXXXXXXXXXQSSKIMKIFKKNKTHSSSSNPPTGKKPEDLLICNLMNELEQKLLAKVNQSMKNPRKSLTPSGKSLESKEKNKFIFPTLNLRKQTSQNSDKDKSEKKFELDEVFEKQKEKKICESPISQKSFDIPDSTPVLTQSVNLRKQSCPNIKLASNESDKNELNTILKKFKVQRISEKD 1700
            METTEYEEGYFKLKKSNEELVTLLNKVINDLKLLKISQKAEKEKN+ALSTSNGNLSSEVIQLTRKCEKQLKTIGDLNNELDYLKSYSKAVEGVAENYCGQTISTQKKYDQLKRQSSIFFNNFQDQSLINIDLNDHESETESCDTPTPILEFEEIKKNHEEILDKEKQKYDILRTELNESQTEVIGLKSEIENANQRLEEKQQDNDKLNQEMDILIKSYSNLKDDHDKMMNYFAPFLRMKAENQELKRTSALLLNNVAGDEKIIEFLSMIEDLKSEISEKNSKISALELQISECEQSTVMLELSTVKSEVDDLARKLESLTKERDTLKHEN+ILLEQKGGFGIAPPPPPPPPPPPPPQSSKIMKIFKKNKTHSSSSNP TGKKPEDLLICNLMNELEQKLLAKVNQSMKNPRKSLTPSGKSLESKEKN+FIFPTLNLRKQTSQNSDKDKSEKKFELDEVFEKQKEKKICESPISQKSFDIPDSTPVLTQSVNLRKQSCPNIKLASNESDKNELNTILKKFKVQRISEKD
Sbjct:    1 METTEYEEGYFKLKKSNEELVTLLNKVINDLKLLKISQKAEKEKNIALSTSNGNLSSEVIQLTRKCEKQLKTIGDLNNELDYLKSYSKAVEGVAENYCGQTISTQKKYDQLKRQSSIFFNNFQDQSLINIDLNDHESETESCDTPTPILEFEEIKKNHEEILDKEKQKYDILRTELNESQTEVIGLKSEIENANQRLEEKQQDNDKLNQEMDILIKSYSNLKDDHDKMMNYFAPFLRMKAENQELKRTSALLLNNVAGDEKIIEFLSMIEDLKSEISEKNSKISALELQISECEQSTVMLELSTVKSEVDDLARKLESLTKERDTLKHENKILLEQKGGFGIAPPPPPPPPPPPPPQSSKIMKIFKKNKTHSSSSNPSTGKKPEDLLICNLMNELEQKLLAKVNQSMKNPRKSLTPSGKSLESKEKNRFIFPTLNLRKQTSQNSDKDKSEKKFELDEVFEKQKEKKICESPISQKSFDIPDSTPVLTQSVNLRKQSCPNIKLASNESDKNELNTILKKFKVQRISEKD 528          
The following BLAST results are available for this feature:
BLAST of SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 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 SMED30030925 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000038398.10.000e+099.24SMESG000038398.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030925 ID=SMED30030925|Name=SMED30030925|organism=Schmidtea mediterranea sexual|type=transcript|length=1925bp
TCTGTATATACATCTGTATAAAATTGACTTAAAATAAACCAATCACATCA
AGGCTATTTTTATGAACTATTAATCAACACTATACTGAATTGCTCATTAA
TTATCATAAATTTTTGATGGAAACTACTGAGTACGAAGAAGGATATTTTA
AACTAAAAAAATCTAACGAAGAATTAGTAACTTTGCTTAATAAAGTTATA
AATGATTTAAAACTTTTAAAAATATCTCAAAAAGCAGAAAAAGAAAAAAA
TGTAGCTTTATCTACATCTAATGGGAACCTGTCCTCAGAAGTTATCCAAT
TAACTAGAAAATGTGAAAAACAATTGAAGACAATAGGTGATCTAAACAAT
GAACTAGATTATTTGAAGTCATATTCCAAAGCAGTAGAGGGCGTCGCTGA
AAACTACTGTGGCCAAACTATTTCTACTCAAAAAAAGTACGATCAATTGA
AACGACAGAGCAGTATATTTTTCAACAATTTCCAAGACCAATCGCTAATT
AACATTGACTTAAATGACCATGAAAGCGAGACTGAGTCCTGCGACACCCC
GACTCCGATTCTTGAATTTGAGGAGATCAAAAAAAACCACGAAGAAATTC
TCGATAAGGAAAAACAGAAATATGATATTTTACGGACAGAGCTAAATGAA
AGTCAAACGGAGGTCATCGGTTTGAAAAGTGAAATTGAAAATGCTAATCA
AAGACTCGAAGAAAAGCAGCAAGACAACGATAAACTAAACCAAGAAATGG
ACATTTTAATCAAATCTTACAGTAATCTTAAAGATGATCATGATAAAATG
ATGAATTATTTTGCCCCTTTTCTCCGAATGAAAGCAGAAAACCAGGAATT
GAAAAGAACGAGTGCTTTACTGTTAAACAATGTTGCAGGCGACGAGAAAA
TCATAGAATTCCTCAGCATGATTGAAGATTTGAAAAGTGAAATTTCAGAG
AAAAATAGCAAAATTTCAGCCCTGGAATTACAAATTTCCGAATGTGAGCA
ATCGACAGTCATGCTTGAACTGTCAACTGTGAAGTCGGAAGTCGACGATC
TGGCACGAAAACTGGAATCTTTGACAAAAGAAAGGGATACTCTAAAACAT
GAAAATAGAATTCTATTGGAACAAAAAGGTGGGTTTGGAATCGCCCCACC
ACCACCACCACCACCGCCACCTCCTCCACCTCCACAATCTTCGAAAATTA
TGAAGATATTCAAAAAAAATAAAACCCATTCAAGCTCTTCGAATCCACCC
ACTGGTAAAAAGCCTGAAGATTTATTGATCTGCAATTTAATGAATGAGCT
CGAACAGAAACTCCTTGCAAAAGTTAATCAAAGCATGAAAAATCCACGAA
AATCACTTACTCCGTCGGGCAAAAGTTTAGAATCTAAAGAAAAAAATAAA
TTCATTTTTCCAACATTAAATCTCCGAAAACAGACATCACAGAATTCCGA
CAAAGACAAGAGTGAAAAGAAATTTGAACTTGACGAAGTGTTTGAAAAAC
AAAAGGAAAAGAAGATATGCGAATCTCCTATCTCGCAAAAAAGTTTCGAT
ATACCCGACAGCACTCCAGTGCTGACACAGTCCGTCAACTTGCGCAAGCA
GTCCTGCCCAAACATAAAATTAGCGTCAAATGAGTCAGATAAGAATGAAC
TAAATACTATTTTAAAAAAGTTTAAAGTGCAGCGCATCAGTGAAAAAGAC
TGAAAAAGACATCAGCTTATTTATATAATTTATTGATTTACAATTTTCTG
AAATTTATTTATTTCAAAATTTTTTTTAAATGTGAACAAAATTGTGTTGA
ATACATTGCGGAAGTTTACTCTGATTGGGCAAACCCTTATATTTGAATCA
ACCAATGAGAATTAAATGCACATTTCGCTTGATGTGATAATCTTTGCCAT
GCCTCAAAGCGATAACTAGATTTGT
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protein sequence of SMED30030925-orf-1

>SMED30030925-orf-1 ID=SMED30030925-orf-1|Name=SMED30030925-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=529bp
METTEYEEGYFKLKKSNEELVTLLNKVINDLKLLKISQKAEKEKNVALST
SNGNLSSEVIQLTRKCEKQLKTIGDLNNELDYLKSYSKAVEGVAENYCGQ
TISTQKKYDQLKRQSSIFFNNFQDQSLINIDLNDHESETESCDTPTPILE
FEEIKKNHEEILDKEKQKYDILRTELNESQTEVIGLKSEIENANQRLEEK
QQDNDKLNQEMDILIKSYSNLKDDHDKMMNYFAPFLRMKAENQELKRTSA
LLLNNVAGDEKIIEFLSMIEDLKSEISEKNSKISALELQISECEQSTVML
ELSTVKSEVDDLARKLESLTKERDTLKHENRILLEQKGGFGIAPPPPPPP
PPPPPPQSSKIMKIFKKNKTHSSSSNPPTGKKPEDLLICNLMNELEQKLL
AKVNQSMKNPRKSLTPSGKSLESKEKNKFIFPTLNLRKQTSQNSDKDKSE
KKFELDEVFEKQKEKKICESPISQKSFDIPDSTPVLTQSVNLRKQSCPNI
KLASNESDKNELNTILKKFKVQRISEKD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000020protonephridia
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000208testis
Vocabulary: INTERPRO
TermDefinition
IPR024849Shootin-1
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 269..296
NoneNo IPR availableCOILSCoilCoilcoord: 302..336
NoneNo IPR availableCOILSCoilCoilcoord: 148..224
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 404..424
NoneNo IPR availablePANTHERPTHR46606:SF3SHOOTIN-1coord: 15..471
IPR024849Shootin-1PANTHERPTHR46606FAMILY NOT NAMEDcoord: 15..471