SMED30002842

Overview
NameSMED30002842
Smed IDSMED30002842
Length (bp)1268
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 SMED30002842 (SMED30002842) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002842 (SMED30002842) 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 SMED30002842 (SMED30002842) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002842 (SMED30002842) 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




SMED30002842

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30002842h1SMcG0010968 PL05017B1C08smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30002842h1SMcG0010968 Contig4448GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30002842h1SMcG0015757 Contig4448GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Smed sexual biotypeSMED30002842h1SMcG0010968 Contig4448GPL15192PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30002842h1SMcG0010968 dd_Smed_v4_8301_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30002842h1SMcG0010968 dd_Smed_v4_8301_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30002842h1SMcG0010968 dd_Smed_v4_8301_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002842h1SMcG0010968 dd_Smed_v4_8301_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002842h1SMcG0015757 Contig4448GPL15192PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30002842h1SMcG0010968 dd_Smed_v6_8301_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30002842h1SMcG0010968 dd_Smed_v4_8301_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
SMED30002842 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000780:30695..32345 +4102
Homology
BLAST of SMED30002842 vs. Planmine SMEST
Match: SMESG000056914.1 (SMESG000056914.1)

HSP 1 Score: 353.599 bits (906), Expect = 5.891e-121
Identity = 222/237 (93.67%), Postives = 226/237 (95.36%), Query Frame = 3
Query:  114 LENRNILLKDEGKLSKIVKTNTSPITLNRKVDEGTLKDITIQNIHDSLLKDYNSLQTMELSEIFLIKLNTVEGFLKFFNNPLQNEILNKIKSKTDFNNYEKTALNCXXXXXXTINMMMKDVSPSIILHVISFVSNYEPYSESNAISRRIVEMSLYCLCNYFEQKNNSTLEKEFLIDYCDALXXXXXXXXXXXXXXXXXXLSFLDTSHLESGVRSDXXXXXXXXXXXXKPPNNGEYFG 824
            L  RN LL DEGKLSKIVKT T+PITLNRKVD+GTLKDI+IQ  HDS+LKDYNSLQTMELSEIFLIKLN VE FLKFFNNPLQNEILNKIKSKTDFNNYEKTALNCISISISTINMMMKDVSPSIILHVISFVSNYEPYSESNAISRRIVEMSLYCLCNYFEQKNNSTLEKEFLIDYCDALIKCFKSKSEKIKISSSIILSFLDTSHLESGVRSDLLR LNYIYLNIKPPN GEYFG
Sbjct:   41 LRKRNNLLNDEGKLSKIVKT-TTPITLNRKVDQGTLKDISIQIFHDSILKDYNSLQTMELSEIFLIKLNRVECFLKFFNNPLQNEILNKIKSKTDFNNYEKTALNCISISISTINMMMKDVSPSIILHVISFVSNYEPYSESNAISRRIVEMSLYCLCNYFEQKNNSTLEKEFLIDYCDALIKCFKSKSEKIKISSSIILSFLDTSHLESGVRSDLLRCLNYIYLNIKPPNKGEYFG 276          
BLAST of SMED30002842 vs. Planmine SMEST
Match: SMESG000056922.1 (SMESG000056922.1)

HSP 1 Score: 49.2914 bits (116), Expect = 2.609e-6
Identity = 36/142 (25.35%), Postives = 71/142 (50.00%), Query Frame = 3
Query:  246 HDSLLKDYNSLQT--MELSEIFLIKLNTVEGFLKFFNNPLQNEILNKIKSKTDFNNYEKTALNCXXXXXXTINMMM------KDVSPSIILHVISFVSNYEPYSESNAISRRIVEMSLYCLCNY---FEQKNNSTLEKEFLI 638
            +++L + Y SL+   +  +E   +    ++ +   F+   Q  IL  IK    F    K A+NC  +S++  ++ +       +++  +I  +I ++  +  + +SN ++RR+VE+ LYCLCN    ++  N   LEK   I
Sbjct:  101 YETLGRLYGSLELEYINFNESKTVTFEDLKRYFLIFDKLWQPSILQTIKENDKFEEIVKLAINCWCVSVNLASLYLFHSLPENNLADDVIKIIIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRI 242          
BLAST of SMED30002842 vs. Planmine SMEST
Match: SMESG000056922.1 (SMESG000056922.1)

HSP 1 Score: 48.9062 bits (115), Expect = 2.959e-6
Identity = 36/142 (25.35%), Postives = 71/142 (50.00%), Query Frame = 3
Query:  246 HDSLLKDYNSLQT--MELSEIFLIKLNTVEGFLKFFNNPLQNEILNKIKSKTDFNNYEKTALNCXXXXXXTINMMM------KDVSPSIILHVISFVSNYEPYSESNAISRRIVEMSLYCLCNY---FEQKNNSTLEKEFLI 638
            +++L + Y SL+   +  +E   +    ++ +   F+   Q  IL  IK    F    K A+NC  +S++  ++ +       +++  +I  +I ++  +  + +SN ++RR+VE+ LYCLCN    ++  N   LEK   I
Sbjct:   95 YETLGRLYGSLELEYINFNESKTVTFEDLKRYFLIFDKLWQPSILQTIKENDKFEEIVKLAINCWCVSVNLASLYLFHSLPENNLADDVIKIIIGYLDAFHSHVQSNGVARRLVEVVLYCLCNACKSYKLSNEEILEKSLRI 236          
The following BLAST results are available for this feature:
BLAST of SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 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 SMED30002842 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000056914.15.891e-12193.67SMESG000056914.1[more]
SMESG000056922.12.609e-625.35SMESG000056922.1[more]
SMESG000056922.12.959e-625.35SMESG000056922.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002842 ID=SMED30002842|Name=SMED30002842|organism=Schmidtea mediterranea sexual|type=transcript|length=1268bp
TTTTTACATCCGTTACTAAGCTTATGATTTAAATAGTCAATTTTCATAAA
TCTTAATTTTGAAATAATATATATTTATTTTGTTATCTCGTGCGGAAAAT
TATGACCCAACTGTTAGAAAACAGGAATATTTTATTAAAGGATGAAGGAA
AACTGTCAAAAATAGTAAAAACTAATACCTCTCCTATTACATTAAATCGA
AAAGTTGATGAAGGCACCTTAAAAGATATTACGATACAGAACATCCATGA
TTCTCTATTAAAAGATTATAACTCCTTACAAACAATGGAATTATCCGAAA
TATTCCTAATCAAATTAAACACAGTGGAAGGTTTTCTAAAATTTTTCAAT
AATCCGTTGCAAAACGAGATCTTAAACAAGATCAAATCGAAAACAGATTT
CAACAATTATGAAAAAACCGCCCTGAATTGCATCAGTATATCAATCAGCA
CAATAAATATGATGATGAAGGATGTTTCACCGTCCATAATTTTGCATGTT
ATTTCATTTGTCAGCAATTATGAACCGTATTCAGAGTCAAATGCGATCTC
TCGGCGCATTGTGGAGATGAGTTTATATTGTCTATGTAATTATTTTGAAC
AGAAAAATAATAGCACGTTAGAAAAAGAATTTCTCATAGATTATTGCGAT
GCGCTAATAAAATGCTTTAAAAGCAAATCTGAAAAAATTAAAATTTCTTC
TTCAATTATTTTATCTTTTCTTGATACGAGTCATTTGGAAAGCGGCGTAA
GATCCGATCTTTTGCGATATTTAAATTATATTTATTTGAACATTAAGCCG
CCGAATAACGGTGAATATTTCGGAATTATTGAGTCACTAATTAGTTCTTC
TATTTCAAGATTGGATAATAATTAATCAATAATAATTATTTAATTGTTTC
AGAAATAAAAAAAGTTATTTATTGATTTAATTAAGAGTAAGAATTTATAT
TTATTTCTAATTGCTTATGAATCCGACTCTTTCGTTCAAGTATTTTGTAC
TTGAACTCCTCCTCACCTTGTATCTTCATAAATGTATATAGAGACAGTGT
GCACTAATTGTTTGTCTCGTATTTTGTTTTTTCGGTCATAGATTTTTGGT
TTTCAGACAAAACAACTTGCATGGAATAATAATAATAATATTATAATTAT
AATTCTGATTATTATGCTGGATTCTCCTTGTTAATAATAATAATAATATT
ATTATTATTGTTGTTGTTATTGGTTGGTTCAATTTTTTGATGTTTCAATA
CTAATTTTTATTTCAGCA
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protein sequence of SMED30002842-orf-1

>SMED30002842-orf-1 ID=SMED30002842-orf-1|Name=SMED30002842-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=258bp
MTQLLENRNILLKDEGKLSKIVKTNTSPITLNRKVDEGTLKDITIQNIHD
SLLKDYNSLQTMELSEIFLIKLNTVEGFLKFFNNPLQNEILNKIKSKTDF
NNYEKTALNCISISISTINMMMKDVSPSIILHVISFVSNYEPYSESNAIS
RRIVEMSLYCLCNYFEQKNNSTLEKEFLIDYCDALIKCFKSKSEKIKISS
SIILSFLDTSHLESGVRSDLLRYLNYIYLNIKPPNNGEYFGIIESLISSS
ISRLDNN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR016024ARM-type_fold
Vocabulary: molecular function
TermDefinition
GO:0005488binding