SMED30021294

Overview
NameSMED30021294
Smed IDSMED30021294
Length (bp)1479
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 SMED30021294 (SMED30021294) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021294 (SMED30021294) 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 SMED30021294 (SMED30021294) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021294 (SMED30021294) 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




SMED30021294

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
intestinal phagocyteSMED30021294h1SMcG0007331 PL08003A1D04smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
muscle cellSMED30021294h1SMcG0007331 dd_Smed_v4_6592_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
enteric muscle cellSMED30021294h1SMcG0007331 dd_Smed_v4_9840_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
enteric muscle cellSMED30021294h1SMcG0007331 dd_Smed_v4_6592_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021294 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008657:1599..5864 -5305
Homology
BLAST of SMED30021294 vs. Planmine SMEST
Match: SMESG000014159.1 (SMESG000014159.1)

HSP 1 Score: 514.227 bits (1323), Expect = 1.155e-177
Identity = 300/300 (100.00%), Postives = 300/300 (100.00%), Query Frame = 3
Query:  429 KDHLNASQSTHITPSIIYRNFNYDSVTPKIAEKTVSXXXXXXXXXXXXXXXXXXXXXCSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLATRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPETNIYTXXXXXXXXXXXXPEYGTMSMTNDTALQANNFEANSXXXXXXXXXXXXQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAVNFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH 1328
            KDHLNASQSTHITPSIIYRNFNYDSVTPKIAEKTVSIEIIYLLTILLCLLLGIITAICSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLATRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPETNIYTSIGSSDNDSSLSPEYGTMSMTNDTALQANNFEANSPYLPPPIEPIRPQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAVNFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH
Sbjct:  353 KDHLNASQSTHITPSIIYRNFNYDSVTPKIAEKTVSIEIIYLLTILLCLLLGIITAICSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLATRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPETNIYTSIGSSDNDSSLSPEYGTMSMTNDTALQANNFEANSPYLPPPIEPIRPQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAVNFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH 652          
BLAST of SMED30021294 vs. Planmine SMEST
Match: SMESG000014159.1 (SMESG000014159.1)

HSP 1 Score: 509.99 bits (1312), Expect = 1.569e-176
Identity = 298/298 (100.00%), Postives = 298/298 (100.00%), Query Frame = 3
Query:  435 HLNASQSTHITPSIIYRNFNYDSVTPKIAEKTVSXXXXXXXXXXXXXXXXXXXXXCSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLATRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPETNIYTXXXXXXXXXXXXPEYGTMSMTNDTALQANNFEANSXXXXXXXXXXXXQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAVNFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH 1328
            HLNASQSTHITPSIIYRNFNYDSVTPKIAEKTVSIEIIYLLTILLCLLLGIITAICSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLATRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPETNIYTSIGSSDNDSSLSPEYGTMSMTNDTALQANNFEANSPYLPPPIEPIRPQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAVNFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH
Sbjct:  323 HLNASQSTHITPSIIYRNFNYDSVTPKIAEKTVSIEIIYLLTILLCLLLGIITAICSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLATRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPETNIYTSIGSSDNDSSLSPEYGTMSMTNDTALQANNFEANSPYLPPPIEPIRPQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAVNFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH 620          
BLAST of SMED30021294 vs. Planmine SMEST
Match: SMESG000014159.1 (SMESG000014159.1)

HSP 1 Score: 509.99 bits (1312), Expect = 2.578e-176
Identity = 298/298 (100.00%), Postives = 298/298 (100.00%), Query Frame = 3
Query:  435 HLNASQSTHITPSIIYRNFNYDSVTPKIAEKTVSXXXXXXXXXXXXXXXXXXXXXCSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLATRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPETNIYTXXXXXXXXXXXXPEYGTMSMTNDTALQANNFEANSXXXXXXXXXXXXQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAVNFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH 1328
            HLNASQSTHITPSIIYRNFNYDSVTPKIAEKTVSIEIIYLLTILLCLLLGIITAICSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLATRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPETNIYTSIGSSDNDSSLSPEYGTMSMTNDTALQANNFEANSPYLPPPIEPIRPQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAVNFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH
Sbjct:  337 HLNASQSTHITPSIIYRNFNYDSVTPKIAEKTVSIEIIYLLTILLCLLLGIITAICSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLATRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPETNIYTSIGSSDNDSSLSPEYGTMSMTNDTALQANNFEANSPYLPPPIEPIRPQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAVNFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH 634          
BLAST of SMED30021294 vs. Planmine SMEST
Match: SMESG000054074.1 (SMESG000054074.1)

HSP 1 Score: 134.42 bits (337), Expect = 2.595e-33
Identity = 68/68 (100.00%), Postives = 68/68 (100.00%), Query Frame = 3
Query:  189 LVKVAHTKKKWKRNRVNSGKKEYYKSNDKAKISLKNTNRIIRTKKLSTKVREFERSNKSSQIEQIESR 392
            LVKVAHTKKKWKRNRVNSGKKEYYKSNDKAKISLKNTNRIIRTKKLSTKVREFERSNKSSQIEQIESR
Sbjct:   15 LVKVAHTKKKWKRNRVNSGKKEYYKSNDKAKISLKNTNRIIRTKKLSTKVREFERSNKSSQIEQIESR 82          
BLAST of SMED30021294 vs. Planmine SMEST
Match: SMESG000054074.1 (SMESG000054074.1)

HSP 1 Score: 134.42 bits (337), Expect = 4.089e-33
Identity = 68/68 (100.00%), Postives = 68/68 (100.00%), Query Frame = 3
Query:  189 LVKVAHTKKKWKRNRVNSGKKEYYKSNDKAKISLKNTNRIIRTKKLSTKVREFERSNKSSQIEQIESR 392
            LVKVAHTKKKWKRNRVNSGKKEYYKSNDKAKISLKNTNRIIRTKKLSTKVREFERSNKSSQIEQIESR
Sbjct:   15 LVKVAHTKKKWKRNRVNSGKKEYYKSNDKAKISLKNTNRIIRTKKLSTKVREFERSNKSSQIEQIESR 82          
The following BLAST results are available for this feature:
BLAST of SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 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 SMED30021294 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014159.11.155e-177100.00SMESG000014159.1[more]
SMESG000014159.11.569e-176100.00SMESG000014159.1[more]
SMESG000014159.12.578e-176100.00SMESG000014159.1[more]
SMESG000054074.12.595e-33100.00SMESG000054074.1[more]
SMESG000054074.14.089e-33100.00SMESG000054074.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021294 ID=SMED30021294|Name=SMED30021294|organism=Schmidtea mediterranea sexual|type=transcript|length=1479bp
AGCAAATGTTTGTAATCTTATAATTAATATAATATATATATAAATCAAAA
AAATATTATATACAATTTATTCAAAAAGGGTTTTGAATTTTTTCTGTATA
TATATATTATCATTCTGCATAGTTTTCACAATTATTTAATACGATTATGT
CTTCATGCAGTTCAGATTTTGAGGACTGTTCAGATGAGCTTGTTAAAGTT
GCTCACACTAAGAAAAAGTGGAAAAGAAATAGAGTTAACAGTGGTAAAAA
GGAATATTACAAATCTAATGACAAAGCCAAAATATCTTTAAAAAATACAA
ATCGTATAATTCGAACGAAAAAACTGAGTACTAAAGTTCGTGAATTCGAA
CGTAGTAATAAATCAAGTCAAATCGAACAAATCGAATCAAGGAATAATAA
TATTAATAATAATAATGATAATAATGACAAAGATCATTTGAATGCTTCCC
AATCCACTCACATTACCCCTTCAATTATCTATCGGAATTTCAACTACGAT
TCTGTAACTCCAAAAATTGCAGAAAAAACTGTCAGCATCGAAATAATATA
TTTACTGACAATTTTATTATGTTTGTTATTGGGTATAATAACGGCAATTT
GCTCATTCTGGATCATAATCAGAAAGCGTCGGTCTAACCAGCGACGCAGT
ATCAAAAAACAGGCCATGGCGTTGTGTTCTCAAACGTCATTTATCCCGTA
CAATCACAATTCGAAAAGCGTCCAGTGTTTACCGAGCTCACTGGCTACTC
GACCAGTTTATCCGTCTTTTACAGTCGATAGACGAAATTATCCCAATGAA
ACGTTTAGGAAAATTTCTCATCCTTCCGGCTCGAATCTTCCTCCGAGTAC
GAGTCTCGATCAAAATGGGTTCATGAGCAAACAATATCTTCCTGAAACCA
ATATCTACACAAGTATTGGAAGTTCAGACAATGATAGTTCATTGAGTCCC
GAATACGGTACGATGAGTATGACTAATGACACAGCTTTACAAGCCAATAA
TTTCGAGGCTAATAGTCCCTATTTACCTCCCCCGATTGAACCCATCCGGC
CTCAAATGTTCAATGATTCATTTATGGACTCGAGTGATTGTCCTTCTTTC
TATTACCCACTTCCAAATACTATTCCAAATATACAAGACCCAACCAATAT
CAATTTCTGGAGATTCAATGGACAAGCATTGACAAGTAAAGCAGTAAACT
TCTCTAGTCAGATGTCTTTCAATGATTTTTCAAAAGACGTAATGAAACTT
GACCAGCAGAACCACCAAGATAATCTGATGAACATTTCGTCAATATATAG
TGATCTACCCCGGATAAATTCCCATCACTGATGATTTACATTCCCATATG
ATATATTACTCCATCAATCAAAAACCAATGAGAAAACTAAGAATTTTGAA
AGAATTTTGTATAAAAATAAATTGAATTATAATATTTCTTTTAATTTGTG
AAGTTTCAGAGCACTCGCTGAAAATGGAG
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protein sequence of SMED30021294-orf-1

>SMED30021294-orf-1 ID=SMED30021294-orf-1|Name=SMED30021294-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=395bp
MSSCSSDFEDCSDELVKVAHTKKKWKRNRVNSGKKEYYKSNDKAKISLKN
TNRIIRTKKLSTKVREFERSNKSSQIEQIESRNNNINNNNDNNDKDHLNA
SQSTHITPSIIYRNFNYDSVTPKIAEKTVSIEIIYLLTILLCLLLGIITA
ICSFWIIIRKRRSNQRRSIKKQAMALCSQTSFIPYNHNSKSVQCLPSSLA
TRPVYPSFTVDRRNYPNETFRKISHPSGSNLPPSTSLDQNGFMSKQYLPE
TNIYTSIGSSDNDSSLSPEYGTMSMTNDTALQANNFEANSPYLPPPIEPI
RPQMFNDSFMDSSDCPSFYYPLPNTIPNIQDPTNINFWRFNGQALTSKAV
NFSSQMSFNDFSKDVMKLDQQNHQDNLMNISSIYSDLPRINSHH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0003104enteric muscle cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 65..85