SMED30031405

Overview
NameSMED30031405
Smed IDSMED30031405
Length (bp)1987
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 SMED30031405 (SMED30031405) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031405 (SMED30031405) 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 SMED30031405 (SMED30031405) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031405 (SMED30031405) 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




SMED30031405

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



PAGE Curations: 17

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30031405SMESG000051910.1 SMESG000051904.1 Contig1775GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v4_298_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v4_298_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v4_298_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermal cellSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v4_298_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
pharynxSMED30031405SMESG000051911.1 dd_Smed_v4_5276_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermal cellSMED30031405SMESG000051911.1 dd_Smed_v4_5276_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
pharynxSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v6_298_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v6_298_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v6_298_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30031405 Contig47021newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v4_298_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v4_298_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30031405SMESG000051910.1 SMESG000051904.1 dd_Smed_v4_298_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30031405SMESG000051911.1 dd_Smed_v4_5276_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30031405SMESG000051911.1 dd_Smed_v4_5276_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30031405SMESG000051911.1 dd_Smed_v4_5276_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
SMED30031405 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004539:34136..36155 +8403
v31.001962:67426..69590 +8143
v31.018242:3088..5569 +6533
Homology
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051904.1 (SMESG000051904.1)

HSP 1 Score: 78.9518 bits (193), Expect = 9.532e-18
Identity = 38/42 (90.48%), Postives = 39/42 (92.86%), Query Frame = 2
Query:   98 MLLRFTTVFFVLAGCFNQMDCGVVGLAVGYSACQTVCNAGYV 223
            MLLRFTTV FVLA CFNQMDCGVVGLAVGYSACQ+ CNAGYV
Sbjct:    1 MLLRFTTVVFVLADCFNQMDCGVVGLAVGYSACQSACNAGYV 42          
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051918.1 (SMESG000051918.1)

HSP 1 Score: 53.5286 bits (127), Expect = 8.545e-9
Identity = 23/41 (56.10%), Postives = 33/41 (80.49%), Query Frame = 2
Query:  101 LLRFTTVFFVLAGCFNQMDCGVVGLAVGYSACQTVCNAGYV 223
            ++R   VF +LA  FNQ++CG++G+ +GY ACQ+VCNAGYV
Sbjct:    1 MIRIAIVFIILASSFNQINCGILGI-LGYGACQSVCNAGYV 40          
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051914.1 (SMESG000051914.1)

HSP 1 Score: 51.9878 bits (123), Expect = 2.291e-8
Identity = 22/41 (53.66%), Postives = 33/41 (80.49%), Query Frame = 2
Query:  101 LLRFTTVFFVLAGCFNQMDCGVVGLAVGYSACQTVCNAGYV 223
            ++R   VF ++A  FNQ++CG++G+ +GY ACQ+VCNAGYV
Sbjct:    1 MIRIAIVFIIVASSFNQINCGILGI-LGYGACQSVCNAGYV 40          
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051910.1 (SMESG000051910.1)

HSP 1 Score: 49.6766 bits (117), Expect = 9.706e-8
Identity = 24/24 (100.00%), Postives = 24/24 (100.00%), Query Frame = 2
Query:  152 MDCGVVGLAVGYSACQTVCNAGYV 223
            MDCGVVGLAVGYSACQTVCNAGYV
Sbjct:    1 MDCGVVGLAVGYSACQTVCNAGYV 24          
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051904.1 (SMESG000051904.1)

HSP 1 Score: 47.3654 bits (111), Expect = 8.212e-7
Identity = 22/24 (91.67%), Postives = 23/24 (95.83%), Query Frame = 2
Query:  152 MDCGVVGLAVGYSACQTVCNAGYV 223
            MDCGVVGLAVGYSACQ+ CNAGYV
Sbjct:    1 MDCGVVGLAVGYSACQSACNAGYV 24          
The following BLAST results are available for this feature:
BLAST of SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 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 SMED30031405 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000051904.19.532e-1890.48SMESG000051904.1[more]
SMESG000051918.18.545e-956.10SMESG000051918.1[more]
SMESG000051914.12.291e-853.66SMESG000051914.1[more]
SMESG000051910.19.706e-8100.00SMESG000051910.1[more]
SMESG000051904.18.212e-791.67SMESG000051904.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031405 ID=SMED30031405|Name=SMED30031405|organism=Schmidtea mediterranea sexual|type=transcript|length=1987bp
CCAGTGAAATAATAGAAATAATAATTTGGAACAGTTTATGAATAGTTTAA
AAATTTTACTATAAAATAGAACATTTTATTTCATTATTTCATTGAAAATG
TTACTACGATTTACAACTGTATTTTTTGTTCTTGCAGGTTGTTTTAATCA
AATGGATTGTGGCGTAGTGGGACTTGCTGTGGGTTATAGCGCATGCCAGA
CTGTCTGCAATGCCGGATATGTCGCATGCTTAGCGTCATTGGGACTAACC
GCAGGAGCGCTTACTGCTGGAGCTGGAGCACTTCCGGCAGTTTTGGCTTG
TTCCGCTGCCCAAGGAGCGTGTATGGCAGCTTGTGCAACCGCATGTGCAG
TAGCTCCTGTATAAACTATAATTTCGAAAACAAGAAACTTTATCTATATT
TTACAAAATGAGTTTTTATCATTTTATGATTTCAAAGGTTTTCTTTAAAT
AAAAGCTGACTTACTCATTTTTGTTACCACTCTGTAATAAGTTTCTCCAG
AACTTATTACGGAAATGTAACAGATCCTTTTAGGGTATATCCATAGGCAT
AATTGCCATTATGCTGTGCATATACCTAATGATTTGGAATTGCAGATGGA
GGGGACAAAGGATGTTGAATAGGATTATTCTCTCCCGTCCAACTACACAA
ATTTCATAACTTTTATAATAGACTTTAGATTGGTATTATTTTAGGCTCGA
ATGGCACGACCAATGGCATCACTCAATTATTGCGATTGGTCAAAATTGAA
ATTAAACATTGGCTGCATCCAGAAATTGAATGTTTATTTTGTCATTTAAT
GACAGCTGGAAATTAATAATAATAGAATAATATATTCCAATAGCAAAGTC
ATTGTCTAAGAATTTTTTTTGAAATTCTACAGTTTGAAAGAATTTAAAAT
TTCCCGCTTTTACTTACCTATTAAATATTTTATTGTGGAATAAATTCGGA
AACGTTTGACATCTTATATCTGGTCATTTGTTCTTTGTATGTCTTGTTAG
GTACACTGAGATTTCGCCGGGGATCTTGTGACGGTCTCCCTTTATATGAA
ATTGAATCTCAAACTGTAATTACATTTAAACAGATTATACTAATTATTTA
ATTATTTAATTTTTCAATCCAAAACGAGATAGCTCCATAAAAAAGGTCTC
ACATCATACTTGTAATCAAGAATTAGATATTATAACAAAGAAGAATTTCT
CACTTCAATGCTTGCACGCTGTTCTTGTCAACTAAATTTCTTCAACCACT
TTGGCAAATTGACTAAAATATATAATTTTTCATAAAGCTCAAGCCTCATC
AATCATTTAATCTCGACTAAACACGCTGCCAATTTACCTGTCAAACTTGG
AGATTTTGTTTACTAATTGAATTGATTAATTCTTATCAACAAATTTATTA
TTCTGCATTTCTTAAATAATATGCTTAGGGACTCCCATTTTTTTATAAAT
AAATATTTATACTCGTTTAAGTTACAAATTCGTAATAAAATTGTCCGTAA
CTTATTATGGAAATGTAAAATTTCTTATTGAGTAATATTTATTACACTTT
GCCTACATTTTTATTGGCGCTAGGAAATGTTTGTTATTTCCGGTTCCCTT
TCTACAGGCTTAGCCCGCATTAATTGCCCGTTTATGACAATCTGTATAAC
GTTTCTCATAACGGCTTAGGTCCGTTTCTTTTAATGAATATATTTATAAA
TTATTAAATATTTTAACTTAATTTTTTATTAAAATAAAAAATTTATTCCT
GAGATTAATATAATGTTTAAATGCTGACTTGAAGACCCCCTTTTCCATTT
TACTCGGTTTTTATTTGTATTTTTTAAAGAAAAATCGGCATTAAATTTGC
TTGAAACTCAAGCTGTTTTAAAGAAAAAGAATTTGAAGTCTTTTTAAGAA
CTTCTAATTTCAGGAGATATATTATATTTTATTTGAAATAATTTTATTAA
ATTAATATTAAATTTTATTTTTATTAATATGAAATAG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000106ciliated epithelial cell
PLANA:0002032epidermal cell
PLANA:0002089reproductive organ
PLANA:0003116parenchymal cell
PLANA:0007528glial cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-TMSignalP-TMcoord: 1..21
score: 0.563
NoneNo IPR availableTMHMMTMhelixcoord: 39..61
NoneNo IPR availableTMHMMTMhelixcoord: 10..32