SMED30012145

Overview
NameSMED30012145
Smed IDSMED30012145
Length (bp)479
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30012145 (SMED30012145) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012145 (SMED30012145) 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.
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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




SMED30012145

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30012145SMESG000053131.1 Contig1320newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30012145SMESG000053131.1 Contig1320uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30012145SMESG000047320.1 Contig1320newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30012145SMESG000047320.1 Contig1320uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
epidermisSMED30012145SMESG000053131.1 dd_Smed_v4_11151_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30012145SMESG000053131.1 dd_Smed_v4_11151_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
SMED30012145 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.018035:9002..9501 -2203
v31.024365:8699..9198 +2112
Homology
BLAST of SMED30012145 vs. Planmine SMEST
Match: SMESG000053131.1 (SMESG000053131.1)

HSP 1 Score: 101.293 bits (251), Expect = 8.988e-29
Identity = 53/60 (88.33%), Postives = 53/60 (88.33%), Query Frame = -3
Query:  223 MATILILGIVFGIICISFFAVVAGICIYKKKSLSKDSRKHHKVRVTQFSPIGSNYDGELG 402
            MATILILGIVFGIICISFFAVV GICIYKKKSLSKDS KHHKVRVTQFSPIGS   G  G
Sbjct:    1 MATILILGIVFGIICISFFAVVVGICIYKKKSLSKDSSKHHKVRVTQFSPIGSCDSGGGG 60          
BLAST of SMED30012145 vs. Planmine SMEST
Match: SMESG000053131.1 (SMESG000053131.1)

HSP 1 Score: 78.1814 bits (191), Expect = 1.143e-19
Identity = 50/54 (92.59%), Postives = 51/54 (94.44%), Query Frame = -3
Query:  241 MATILILGIVFGIICISFFAVVAGICIYKKKSLSKDSRKHHKVRVTQFSPIGSN 402
            MATILILGIVFGIICISFFAVV GICIYKKKSLSKDS KHHKVRVTQFSPIG+ 
Sbjct:    1 MATILILGIVFGIICISFFAVVVGICIYKKKSLSKDSSKHHKVRVTQFSPIGNR 54          
The following BLAST results are available for this feature:
BLAST of SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 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 SMED30012145 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000053131.18.988e-2988.33SMESG000053131.1[more]
SMESG000053131.11.143e-1992.59SMESG000053131.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012145 ID=SMED30012145|Name=SMED30012145|organism=Schmidtea mediterranea sexual|type=transcript|length=479bp
TCAAATAATTTTTGTGAAATATATTTTATTGGATATTTTGTACCACATTA
CCACATCAACTGCACGAAACAAATTTAAAAAATACCTGGAAAATGAAACT
TATTATTTAAAGGTAAAAATCCATTAATTCTAATCTCAACAACCTCCTTA
ATCACATCCTCCATCTCCTGAATCACAGCCTCCTCCTCCTCCTGAATCAC
AATCTATTCCGTTAATCCAAAGACCTAATTCACCATCATAATTACTTCCA
ATTGGCGAAAATTGTGTAACACGAACTTTGTGATGTTTACGAGAATCTTT
TGATAAAGATTTCTTTTTATAAATACAAATTCCAGCAACAACGGCGAAAA
ATGAAATACATATTATTCCGAAAACTATTCCTAAAATTAGAATTGTTGCC
ATTCAATTATTCAAAATAATTCTAGATTTTAATTGTCGACATTAATATGA
GTGCTTTCAATGATGTTTGTTCACTGAAC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000070intestinal phagocyte
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 4..26