SMED30017313

Overview
NameSMED30017313
Smed IDSMED30017313
Length (bp)336
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 SMED30017313 (SMED30017313) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017313 (SMED30017313) 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



SMED30017313

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30017313SMESG000016774.1 SMESG000016773.1 SMESG000016788.1 SMESG000016784.1 SMESG000016778.1 Contig3437GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017313SMESG000016788.1 SMESG000016782.1 SMESG000016778.1 SMESG000016774.1 SMESG000016773.1 SMED_21625_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017313SMESG000016788.1 SMESG000016782.1 SMESG000016778.1 SMESG000016774.1 SMESG000016773.1 SMED_21625_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017313SMESG000016788.1 SMESG000016784.1 SMESG000016778.1 SMED_21625_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017313SMESG000016788.1 SMESG000016784.1 SMESG000016778.1 SMED_21625_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017313 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002808:51727..52103 +1289
v31.015040:11928..12304 -1275
v31.007135:759..2073 -1254
v31.007135:5122..5498 -1217
v31.015040:10171..10435 +840
v31.007135:3247..3513 +806
Homology
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BLAST of SMED30017313 vs. Planmine SMEST
Match: SMESG000016788.1 (SMESG000016788.1)

HSP 1 Score: 83.1889 bits (204), Expect = 2.014e-34
Identity = 41/49 (83.67%), Postives = 41/49 (83.67%), Query Frame = 1 
Query:   61 NSNGEPVKRFQXNANPSMSIXAXKRNLSXKNGGDIQSVXFXGETLSDXK 207
            NSNGEPVKRFQ NANPSMSI A KRNLS K GGDIQSV F GETLSD K
Sbjct:   12 NSNGEPVKRFQVNANPSMSISALKRNLSDKYGGDIQSVRFNGETLSDDK 60

HSP 2 Score: 78.9518 bits (193), Expect = 2.014e-34
Identity = 37/47 (78.72%), Postives = 40/47 (85.11%), Query Frame = 3 
Query:  195 IRXQETCNFYNIRDGATLELIFNKQDSQINLIVEGQSQTGNQKPIPV 335
            +   + CNFYNIRDGATLELIFNK DSQINLIVE QS+TGNQKPI V
Sbjct:   56 LSDDKNCNFYNIRDGATLELIFNKPDSQINLIVEVQSETGNQKPISV 102
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BLAST of SMED30017313 vs. Planmine SMEST
Match: SMESG000016784.1 (SMESG000016784.1)

HSP 1 Score: 81.6481 bits (200), Expect = 6.191e-34
Identity = 40/49 (81.63%), Postives = 40/49 (81.63%), Query Frame = 1 
Query:   61 NSNGEPVKRFQXNANPSMSIXAXKRNLSXKNGGDIQSVXFXGETLSDXK 207
            NSNGEPVKRFQ NANPSMSI   KRNLS K GGDIQSV F GETLSD K
Sbjct:   12 NSNGEPVKRFQVNANPSMSISVLKRNLSDKYGGDIQSVRFNGETLSDDK 60

HSP 2 Score: 78.9518 bits (193), Expect = 6.191e-34
Identity = 37/47 (78.72%), Postives = 40/47 (85.11%), Query Frame = 3 
Query:  195 IRXQETCNFYNIRDGATLELIFNKQDSQINLIVEGQSQTGNQKPIPV 335
            +   + CNFYNIRDGATLELIFNK DSQINLIVE QS+TGNQKPI V
Sbjct:   56 LSDDKNCNFYNIRDGATLELIFNKPDSQINLIVEVQSETGNQKPISV 102
[Close]
BLAST of SMED30017313 vs. Planmine SMEST
Match: SMESG000016778.1 (SMESG000016778.1)

HSP 1 Score: 78.5666 bits (192), Expect = 5.892e-30
Identity = 37/43 (86.05%), Postives = 39/43 (90.70%), Query Frame = 3 
Query:  207 ETCNFYNIRDGATLELIFNKQDSQINLIVEGQSQTGNQKPIPV 335
            + CNFYNIRDGATLELIFNK DSQINLIVE QS+TGNQKPI V
Sbjct:   60 KNCNFYNIRDGATLELIFNKPDSQINLIVEVQSETGNQKPISV 102

HSP 2 Score: 68.5514 bits (166), Expect = 5.892e-30
Identity = 36/49 (73.47%), Postives = 37/49 (75.51%), Query Frame = 1 
Query:   61 NSNGEPVKRFQXNANPSMSIXAXKRNLSXKNGGDIQSVXFXGETLSDXK 207
            NSN E +KR Q NANPSMSI A KRNLS K GGDIQSV F  ETLSD K
Sbjct:   12 NSNQELLKRDQVNANPSMSISALKRNLSDKYGGDIQSVRFNSETLSDDK 60
[Close]
BLAST of SMED30017313 vs. Planmine SMEST
Match: SMESG000016782.1 (SMESG000016782.1)

HSP 1 Score: 81.2629 bits (199), Expect = 1.311e-29
Identity = 38/43 (88.37%), Postives = 40/43 (93.02%), Query Frame = 3 
Query:  207 ETCNFYNIRDGATLELIFNKQDSQINLIVEGQSQTGNQKPIPV 335
            + CNFYNIRDGATLELIFNK DSQINLIVE QS+TGNQKPIPV
Sbjct:   60 KNCNFYNIRDGATLELIFNKPDSQINLIVEVQSETGNQKPIPV 102

HSP 2 Score: 64.3142 bits (155), Expect = 1.311e-29
Identity = 33/49 (67.35%), Postives = 36/49 (73.47%), Query Frame = 1 
Query:   61 NSNGEPVKRFQXNANPSMSIXAXKRNLSXKNGGDIQSVXFXGETLSDXK 207
            NSNGEP+KR Q N + SMSI A KRN +  N GDIQSV F GETLSD K
Sbjct:   12 NSNGEPIKREQVNVSSSMSISALKRNWADINDGDIQSVRFNGETLSDDK 60
[Close]
BLAST of SMED30017313 vs. Planmine SMEST
Match: SMESG000016774.1 (SMESG000016774.1)

HSP 1 Score: 75.485 bits (184), Expect = 2.776e-29
Identity = 36/41 (87.80%), Postives = 37/41 (90.24%), Query Frame = 3 
Query:  213 CNFYNIRDGATLELIFNKQDSQINLIVEGQSQTGNQKPIPV 335
            CNFYNIRDGATLELIFNK DSQINL VE QS+TGNQKPI V
Sbjct:   62 CNFYNIRDGATLELIFNKPDSQINLSVEVQSETGNQKPISV 102

HSP 2 Score: 69.3218 bits (168), Expect = 2.776e-29
Identity = 36/47 (76.60%), Postives = 37/47 (78.72%), Query Frame = 1 
Query:   61 NSNGEPVKRFQXNANPSMSIXAXKRNLSXKNGGDIQSVXFXGETLSD 201
            NSN E +KR Q NANPSMSI A KRNLS K GGDIQSV F GETLSD
Sbjct:   12 NSNRELLKRDQVNANPSMSISALKRNLSDKYGGDIQSVRFNGETLSD 58
The following BLAST results are available for this feature:
BLAST of SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 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 SMED30017313 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016788.12.014e-3483.67SMESG000016788.1[more]
SMESG000016784.16.191e-3481.63SMESG000016784.1[more]
SMESG000016778.15.892e-3086.05SMESG000016778.1[more]
SMESG000016782.11.311e-2988.37SMESG000016782.1[more]
SMESG000016774.12.776e-2987.80SMESG000016774.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017313 ID=SMED30017313|Name=SMED30017313|organism=Schmidtea mediterranea sexual|type=transcript|length=336bp
TCAAGTTTTTTTTTTTTTAAAAAGCTANGGANAANATTAANCTGGGCCNG
CAAGTCGCGGAATTCAAATGGAGAACCAGTAAAAAGATTCCAAGNGAATG
CCAACCCTTCGATGTCAATAAGNGCATNAAAAAGGAATTTGTCAGNCAAA
AACGGTGGGGACATCCAATCAGTGCNATTCNACGGTGAAACGTTATCCGA
TGNCAAGAAACNTGCAATTTTTATAACATCCGAGATGGGGCAACACTGGA
ACTCATTTTTAATAAACAAGACAGCCAGATTAACCTCATTGTGGAAGGGC
AATCACAAACTGGAAATCAGAAACCTATTCCAGTAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000429neoblast