SMED30029525

Overview
NameSMED30029525
Smed IDSMED30029525
Length (bp)259
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 SMED30029525 (SMED30029525) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029525 (SMED30029525) 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




SMED30029525

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30029525SMESG000074822.1 SmedASXL_014045SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30029525SMESG000074822.1 dd_Smed_v4_15474_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30029525SMESG000074822.1 dd_Smed_v4_15474_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
Homology
BLAST of SMED30029525 vs. Ensembl Celegans
Match: egl-4 (cGMP-dependent protein kinase egl-4 [Source:UniProtKB/Swiss-Prot;Acc:O76360])

HSP 1 Score: 43.8986 bits (102), Expect = 2.265e-6
Identity = 19/42 (45.24%), Postives = 25/42 (59.52%), Query Frame = 1
Query:    4 SKEMTPVIIPKLENNIDTHYFDQFTEKNFVPLDETSGWDDEF 129
            S+ + P I+PK+ N  D   FD +   N VP DE SGWD+ F
Sbjct:  708 SRTLKPPILPKVSNPADVTNFDNYPPDNDVPPDEFSGWDEGF 749          
BLAST of SMED30029525 vs. Ensembl Celegans
Match: egl-4 (cGMP-dependent protein kinase egl-4 [Source:UniProtKB/Swiss-Prot;Acc:O76360])

HSP 1 Score: 43.8986 bits (102), Expect = 2.265e-6
Identity = 19/42 (45.24%), Postives = 25/42 (59.52%), Query Frame = 1
Query:    4 SKEMTPVIIPKLENNIDTHYFDQFTEKNFVPLDETSGWDDEF 129
            S+ + P I+PK+ N  D   FD +   N VP DE SGWD+ F
Sbjct:  708 SRTLKPPILPKVSNPADVTNFDNYPPDNDVPPDEFSGWDEGF 749          
BLAST of SMED30029525 vs. Ensembl Celegans
Match: egl-4 (cGMP-dependent protein kinase egl-4 [Source:UniProtKB/Swiss-Prot;Acc:O76360])

HSP 1 Score: 43.8986 bits (102), Expect = 2.265e-6
Identity = 19/42 (45.24%), Postives = 25/42 (59.52%), Query Frame = 1
Query:    4 SKEMTPVIIPKLENNIDTHYFDQFTEKNFVPLDETSGWDDEF 129
            S+ + P I+PK+ N  D   FD +   N VP DE SGWD+ F
Sbjct:  708 SRTLKPPILPKVSNPADVTNFDNYPPDNDVPPDEFSGWDEGF 749          
BLAST of SMED30029525 vs. Ensembl Celegans
Match: egl-4 (cGMP-dependent protein kinase egl-4 [Source:UniProtKB/Swiss-Prot;Acc:O76360])

HSP 1 Score: 43.8986 bits (102), Expect = 2.332e-6
Identity = 19/42 (45.24%), Postives = 25/42 (59.52%), Query Frame = 1
Query:    4 SKEMTPVIIPKLENNIDTHYFDQFTEKNFVPLDETSGWDDEF 129
            S+ + P I+PK+ N  D   FD +   N VP DE SGWD+ F
Sbjct:  702 SRTLKPPILPKVSNPADVTNFDNYPPDNDVPPDEFSGWDEGF 743          
BLAST of SMED30029525 vs. Ensembl Celegans
Match: egl-4 (cGMP-dependent protein kinase egl-4 [Source:UniProtKB/Swiss-Prot;Acc:O76360])

HSP 1 Score: 43.8986 bits (102), Expect = 2.332e-6
Identity = 19/42 (45.24%), Postives = 25/42 (59.52%), Query Frame = 1
Query:    4 SKEMTPVIIPKLENNIDTHYFDQFTEKNFVPLDETSGWDDEF 129
            S+ + P I+PK+ N  D   FD +   N VP DE SGWD+ F
Sbjct:  702 SRTLKPPILPKVSNPADVTNFDNYPPDNDVPPDEFSGWDEGF 743          
BLAST of SMED30029525 vs. Planmine SMEST
Match: SMESG000074822.1 (SMESG000074822.1)

HSP 1 Score: 98.2117 bits (243), Expect = 1.947e-25
Identity = 45/45 (100.00%), Postives = 45/45 (100.00%), Query Frame = 1
Query:    1 LSKEMTPVIIPKLENNIDTHYFDQFTEKNFVPLDETSGWDDEFEF 135
            LSKEMTPVIIPKLENNIDTHYFDQFTEKNFVPLDETSGWDDEFEF
Sbjct:  735 LSKEMTPVIIPKLENNIDTHYFDQFTEKNFVPLDETSGWDDEFEF 779          
The following BLAST results are available for this feature:
BLAST of SMED30029525 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 SMED30029525 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 5
Match NameE-valueIdentityDescription
egl-42.265e-645.24cGMP-dependent protein kinase egl-4 [Source:UniPr... [more]
egl-42.265e-645.24cGMP-dependent protein kinase egl-4 [Source:UniPr... [more]
egl-42.265e-645.24cGMP-dependent protein kinase egl-4 [Source:UniPr... [more]
egl-42.332e-645.24cGMP-dependent protein kinase egl-4 [Source:UniPr... [more]
egl-42.332e-645.24cGMP-dependent protein kinase egl-4 [Source:UniPr... [more]
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BLAST of SMED30029525 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 SMED30029525 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 SMED30029525 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 SMED30029525 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 SMED30029525 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 SMED30029525 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 SMED30029525 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 SMED30029525 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 SMED30029525 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 SMED30029525 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 SMED30029525 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 SMED30029525 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000074822.11.947e-25100.00SMESG000074822.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029525 ID=SMED30029525|Name=SMED30029525|organism=Schmidtea mediterranea sexual|type=transcript|length=259bp
TTATCTAAAGAAATGACTCCAGTAATTATTCCAAAACTTGAAAATAATAT
TGATACTCACTATTTCGATCAATTTACAGAAAAAAACTTTGTACCCCTCG
ATGAAACTTCAGGATGGGATGATGAATTTGAATTTTAATCATATTTTGTA
TGTATAATTTGTTTGTTTTCTAGAGAGATATTTTCTGTAATAAATATTAT
TTTTACTAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANAAAAAAA
AANAAAAAA
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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:0000418head