SMED30022130

Overview
NameSMED30022130
Smed IDSMED30022130
Length (bp)450
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 SMED30022130 (SMED30022130) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022130 (SMED30022130) 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



SMED30022130

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30022130SMESG000026848.1 dd_Smed_v4_1128_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022130SMESG000026848.1 dd_Smed_v4_1128_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30022130SMESG000026848.1 dd_Smed_v6_1128_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
gutSMED30022130SMESG000026848.1 SMED30022130smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30022130SMESG000026848.1 SMED30022130smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Category 3 cellSMED30022130SMESG000026848.1 dd_Smed_v6_1128_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30022130SMESG000026848.1 dd_Smed_v4_1128_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
SMED30022130 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000000:541958..542403 -2172
Homology
[Close]
BLAST of SMED30022130 vs. Planmine SMEST
Match: SMESG000026848.1 (SMESG000026848.1)

HSP 1 Score: 101.679 bits (252), Expect = 7.196e-29
Identity = 47/47 (100.00%), Postives = 47/47 (100.00%), Query Frame = -3 
Query:  110 DDSLANIDETMCPNLIYKYCRGPHCLTCTIKCEKVDGECQKKSAECV 250
            DDSLANIDETMCPNLIYKYCRGPHCLTCTIKCEKVDGECQKKSAECV
Sbjct:   40 DDSLANIDETMCPNLIYKYCRGPHCLTCTIKCEKVDGECQKKSAECV 86

HSP 2 Score: 75.485 bits (184), Expect = 1.298e-18
Identity = 43/66 (65.15%), Postives = 48/66 (72.73%), Query Frame = -2 
Query:  258 MKLTISIITLFVVIPLFSGALLRVQKKEKFVGTEFGMHSLWKILKKTLYSI---ILINISYFYSRG 446
            MKLTISIITLFVVIPLFSGALLRVQKKEKFVGTEF      + L  +L +I   +  N+ Y Y RG
Sbjct:    1 MKLTISIITLFVVIPLFSGALLRVQKKEKFVGTEF-----EEFLDDSLANIDETMCPNLIYKYCRG 61
The following BLAST results are available for this feature:
BLAST of SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 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 SMED30022130 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000026848.17.196e-29100.00SMESG000026848.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022130 ID=SMED30022130|Name=SMED30022130|organism=Schmidtea mediterranea sexual|type=transcript|length=450bp
TTTTTCAAAGTGAAATTATTTATTCAGTACAAAAATATTATACATTCAAA
CAAAAACTCAATTAAAAAATATCCTATTTCGTGAGATACCAAAGATTTTT
TAAATTTTAAACACATTCAGCAGATTTCTTCTGGCACTCTCCGTCGACTT
TTTCACATTTAATTGTACAAGTCAAGCAGTGGGGGCCCCTGCAGTATTTG
TAGATCAAATTCGGGCACATTGTCTCATCAATGTTTGCTAAAGAATCATC
CAAAAATTCCTCTAGAATAAAAATAAGAAATATTAATTAAAATGATACTA
TAGAGAGTTTTTTTTAAAATCTTCCAGAGAGAATGCATACCGAATTCTGT
TCCGACGAATTTTTCCTTTTTCTGTACTCTCAATAGTGCACCGGAAAATA
GAGGAATGACGACAAAAAGAGTGATAATGCTGATTGTGAGCTTCATGATT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000035Category 3 cell
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0002142parenchyma