SMED30010231

Overview
NameSMED30010231
Smed IDSMED30010231
Length (bp)377
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 SMED30010231 (SMED30010231) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010231 (SMED30010231) 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



SMED30010231

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
pharynxSMED30010231 dd_Smed_v4_10874_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30010231 dd_Smed_v4_10874_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30010231 dd_Smed_v4_10874_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30010231 dd_Smed_v4_10874_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30010231 dd_Smed_v4_10874_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30010231 dd_Smed_v4_10874_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30010231 dd_Smed_v6_10874_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30010231 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.028031:1744..4116 -1729
v31.032769:2675..3044 -1052
Homology
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BLAST of SMED30010231 vs. Planmine SMEST
Match: SMESG000015125.1 (SMESG000015125.1)

HSP 1 Score: 110.923 bits (276), Expect = 3.951e-33
Identity = 52/71 (73.24%), Postives = 60/71 (84.51%), Query Frame = -3 
Query:  139 MPNDYYITYPGNSIVVLDKAIQKDMSVSTEYDGSHFTIICDGKIYLTKFTKDIHVAGKEVKDGRITIKYSV 351
            MPN+Y I+Y  NS++V DK I+  M V T+++GSHFTIICDGKIYLTKFT DI VAGKEVKDGRITIKYSV
Sbjct:    1 MPNEYQISYLANSVIVRDKEIESGMKVDTKFNGSHFTIICDGKIYLTKFTNDIQVAGKEVKDGRITIKYSV 71
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BLAST of SMED30010231 vs. Planmine SMEST
Match: SMESG000015118.1 (SMESG000015118.1)

HSP 1 Score: 110.538 bits (275), Expect = 7.712e-33
Identity = 53/75 (70.67%), Postives = 63/75 (84.00%), Query Frame = -3 
Query:  127 MPNDYYITYPGNSIVVLDKAIQKDMSVSTEYDGSHFTIICDGKIYLTKFTKDIHVAGKEVKDGRITIKYSV*IDI 351
            MPN+Y I+Y GNS++V DK I+  M V T+++GSHFTIIC+ KIYLTKF  DIHV+GKEVKDGRITIKYSV IDI
Sbjct:    1 MPNEYQISYLGNSVIVRDKEIESGMKVDTKFNGSHFTIICEDKIYLTKFINDIHVSGKEVKDGRITIKYSVLIDI 75
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BLAST of SMED30010231 vs. Planmine SMEST
Match: SMESG000015116.1 (SMESG000015116.1)

HSP 1 Score: 87.8113 bits (216), Expect = 6.471e-24
Identity = 46/69 (66.67%), Postives = 53/69 (76.81%), Query Frame = -3 
Query:  151 MPNDYYITYPGNSIVVLDKAIQKDMSVSTEYDG--SHFTIICDGKIYLTKFTKDIHVAGKEVKDGRITI 351
            MPND +ITYPGNSIVVLDKAIQ+DMSVSTEYDG  S F IIC  K Y TKF  +  V   +V++G+ITI
Sbjct:    1 MPNDCHITYPGNSIVVLDKAIQQDMSVSTEYDGSCSRFVIICGDKTYETKFDVNKEVTETKVENGKITI 69
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BLAST of SMED30010231 vs. Planmine SMEST
Match: SMESG000015124.1 (SMESG000015124.1)

HSP 1 Score: 60.4622 bits (145), Expect = 9.906e-13
Identity = 27/35 (77.14%), Postives = 33/35 (94.29%), Query Frame = -3 
Query:  247 MPNDYYITYPGNSIVVLDKAIQKDMSVSTEYDGSH 351
            MP+DYYITY GNSI+VLDKAIQ+DMSVST++D S+
Sbjct:    1 MPDDYYITYQGNSILVLDKAIQQDMSVSTKFDVSY 35
The following BLAST results are available for this feature:
BLAST of SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 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 SMED30010231 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000015125.13.951e-3373.24SMESG000015125.1[more]
SMESG000015118.17.712e-3370.67SMESG000015118.1[more]
SMESG000015116.16.471e-2466.67SMESG000015116.1[more]
SMESG000015124.19.906e-1377.14SMESG000015124.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010231 ID=SMED30010231|Name=SMED30010231|organism=Schmidtea mediterranea sexual|type=transcript|length=377bp
TAATCCTAAATATATTATATTAAATATTTAACTAAATACATTTTATAAGG
TTTTAAATATATAAAAATGTTGAGAATAACAAAATCTAAAATAAAATGTT
ACAGTGACGATAAAAAGAATTTCTCAGATGTCAATTTAGACAGAATATTT
AATAGTTATTCTTCCATCTTTTACTTCCTTTCCAGCAACATGAATGTCCT
TTGTGAACTTTGTCAAATATATTTTGCCGTCACAAATTATTGTGAAATGT
GATCCGTCATATTCAGTCGATACACTCATGTCTTTCTGAATCGCTTTGTC
AAGCACAACGATAGAATTTCCTGGGTATGTAATATAATAATCGTTCGGCA
TGATCAAATAAATTACTTAATCTCCCC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx