SMED30007241

Overview
NameSMED30007241
Smed IDSMED30007241
Length (bp)1346
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 SMED30007241 (SMED30007241) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007241 (SMED30007241) 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 SMED30007241 (SMED30007241) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007241 (SMED30007241) 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




SMED30007241

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30007241SMESG000077709.1 SMESG000073947.1 SMESG000043656.1 SMESG000043279.1 SMESG000008519.1 SMESG000001897.1 Contig22newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
dorsal ventral margin of the whole animalSMED30007241SMESG000077709.1 SMESG000073947.1 SMESG000043656.1 SMESG000043279.1 SMESG000008519.1 SMESG000001897.1 Contig22newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30007241SMESG000077709.1 SMESG000073947.1 SMESG000043656.1 SMESG000043279.1 SMESG000008519.1 SMESG000001897.1 Contig22newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30007241SMESG000077709.1 SMESG000073947.1 SMESG000043656.1 SMESG000043279.1 SMESG000008519.1 SMESG000001897.1 Contig19newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30007241SMESG000013795.1 Contig22newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
dorsal ventral margin of the whole animalSMED30007241SMESG000013795.1 Contig22newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30007241SMESG000013795.1 Contig22newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30007241SMESG000007852.1 Contig19newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
cephalic gangliaSMED30007241 dd_Smed_v4_19475_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30007241 dd_Smed_v4_19475_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30007241 dd_Smed_v4_19475_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30007241 dd_Smed_v4_19475_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30007241 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001683:88492..89839 +6571
Homology
BLAST of SMED30007241 vs. Planmine SMEST
Match: SMESG000046598.1 (SMESG000046598.1)

HSP 1 Score: 55.0694 bits (131), Expect = 5.380e-9
Identity = 29/60 (48.33%), Postives = 37/60 (61.67%), Query Frame = 1
Query:  718 KTIKQPIVECPIENRQVMVMFGI*ADFNLISEELCEDIKKQKGAIKVYESNTKIRYVNIS 897
            KT  +P+ EC I N+QV V+F   AD N+IS+EL  DI K   A +VY S TK+   N S
Sbjct:   87 KTRNKPVTECAIRNQQVKVLFDSGADLNVISQELMSDIVKDNPAQRVYNSTTKVTCANGS 146          
The following BLAST results are available for this feature:
BLAST of SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 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 SMED30007241 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000046598.15.380e-948.33SMESG000046598.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007241 ID=SMED30007241|Name=SMED30007241|organism=Schmidtea mediterranea sexual|type=transcript|length=1346bp
GACTTGTGAGCTTAGTCGACTTGTAAAGAAGAATCAGAATGAGATTTATT
AACTGGAAAAATGATCGTTTTTATTAAAGGAGTTCCAAGCAGGCACACAG
AAAGCGCTTTAAAGTTTGCTATGCCGAAAACATTAGAAGAAGCTATGGAG
AAAGTGAAAACAAAAAAGCAAATTGAAAATGTCTACAGAAAAAAACAAGT
TTGTTGTAATGCTCAGAAAGGTAAAATCGAAAAATTTGAAAAAATTAAAA
TATTAATAAAAGAAATTGTAATGTTAAAGAGAAGAAGCTGGAGTCGAACA
GATCAACGTCAACTGAGAGGAAAGAATACTAGAATATGTATTAAATGTGA
CAAAATAGGGCATATAGCCAGATTTTGCACATAACTACAAAGTAACATTA
TAACATCAATCAAATGTTTTAAATATGGTGGAAAGCATTTAATCAAAGAT
TGTAAACCCAGAATCGTTTTCATTATTTTCAGGAAGAAGTGGATAGTAAA
ACCTATTCAGTTATTGAAACAATAAGCGAAAATGATTATAAAAGTCTAAA
TGTTATCAATGAGTGGGACATAAAGATAACAACTAAAGCTATTAAAAACT
TTAAAATGCAACTCATATCGGAAGAATAATATGAAAATTTTACAAATGGT
GAAGCCGCAAAACCGAGAAAACAACTTTATGAATACCAGGAGACTTTAAT
TTCGAATAGAGAAACGAAAAACCATAAAGCAACCAATTGTTGAATGCCCA
ATAGAGAATCGTCAAGTAATGGTGATGTTTGGTATATGAGCTGATTTTAA
TCTCATCAGCGAAGAATTATGTGAGGATATAAAGAAGCAAAAGGGTGCTA
TTAAAGTATATGAAAGCAACACTAAGATTAGATATGTAAATATTAGTGAA
GTAAACTGTATTAGAAAAGTGCAATTAAACGTTGAAATAGCATCAGTTTT
AACAAATCACGTATTTGATATTATGTTAAATATTTCCCCTCATTTATATA
TTGGATCAGAAGCATGACTAAATATGAAATAAAAGTGAATCCCTCGGAAA
AATTAAGGAATCAAAGCTCCGGTTATATCAGAATCTGTATTACCAGCTTT
AAAATAATATCTACCGCGGTAGTGAGCCGAATACGGTTAATAAAGTTCGT
AATTTATCTTATAATAATTATTATAGAGTGATTTTTGGCAAGTAATATAG
ATATAACCAATGTGGGGGAATAATACTGTTGAGGATACCTAAATAATAGA
GTAAAATAATTAATAAACATGTAAAATGATTGGGGAAACAATGATAAGTG
ATTAATATGTGGTTCTGGAGCGTAATAAAAAGGGAATGAAAAAGAA
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protein sequence of SMED30007241-orf-1

>SMED30007241-orf-1 ID=SMED30007241-orf-1|Name=SMED30007241-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
MIVFIKGVPSRHTESALKFAMPKTLEEAMEKVKTKKQIENVYRKKQVCCN
AQKGKIEKFEKIKILIKEIVMLKRRSWSRTDQRQLRGKNTRICIKCDKIG
HIARFCT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000070intestinal phagocyte
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0002056medial muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR036875Znf_CCHC_sf
IPR001878Znf_CCHC
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0003676nucleic acid binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036875Zinc finger, CCHC-type superfamilySUPERFAMILYSSF57756Retrovirus zinc finger-like domainscoord: 74..106