SMED30029399

Overview
NameSMED30029399
Smed IDSMED30029399
Length (bp)251
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 SMED30029399 (SMED30029399) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029399 (SMED30029399) 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



SMED30029399

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30029399 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 systemSMED30029399 dd_Smed_v4_10874_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30029399 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 gangliaSMED30029399 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 neuronSMED30029399 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 neuronSMED30029399 dd_Smed_v4_10874_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029399 Contig41082newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029399 Contig41082uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029399 Contig13501newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029399 Contig13501uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30029399 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
SMED30029399 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.017217:1168..3055 -1201
v31.029841:4207..6107 +1183
v31.025823:358..1548 +1076
v31.022945:305..1496 +1067
v31.049210:1..1149 +1021
Homology
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BLAST of SMED30029399 vs. Planmine SMEST
Match: SMESG000015116.1 (SMESG000015116.1)

HSP 1 Score: 137.502 bits (345), Expect = 2.452e-44
Identity = 67/68 (98.53%), Postives = 68/68 (100.00%), Query Frame = 2 
Query:   47 HITYPGNSIVVLDKAIQQDMSVSTEYDGSCSRFVIICGDKTYKTKFDVNKEVTETKVENGKITIICSN 250
            HITYPGNSIVVLDKAIQQDMSVSTEYDGSCSRFVIICGDKTY+TKFDVNKEVTETKVENGKITIICSN
Sbjct:    6 HITYPGNSIVVLDKAIQQDMSVSTEYDGSCSRFVIICGDKTYETKFDVNKEVTETKVENGKITIICSN 73
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BLAST of SMED30029399 vs. Planmine SMEST
Match: SMESG000015118.1 (SMESG000015118.1)

HSP 1 Score: 55.4546 bits (132), Expect = 7.521e-12
Identity = 30/63 (47.62%), Postives = 43/63 (68.25%), Query Frame = 2 
Query:   50 ITYPGNSIVVLDKAIQQDMSVSTEYDGSCSRFVIICGDKTYKTKFDVNKEVTETKVENGKITI 238
            I+Y GNS++V DK I+  M V T+++GS   F IIC DK Y TKF  +  V+  +V++G+ITI
Sbjct:    7 ISYLGNSVIVRDKEIESGMKVDTKFNGS--HFTIICEDKIYLTKFINDIHVSGKEVKDGRITI 67
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BLAST of SMED30029399 vs. Planmine SMEST
Match: SMESG000015125.1 (SMESG000015125.1)

HSP 1 Score: 51.9878 bits (123), Expect = 2.006e-10
Identity = 28/64 (43.75%), Postives = 41/64 (64.06%), Query Frame = 2 
Query:   47 HITYPGNSIVVLDKAIQQDMSVSTEYDGSCSRFVIICGDKTYKTKFDVNKEVTETKVENGKITI 238
             I+Y  NS++V DK I+  M V T+++GS   F IIC  K Y TKF  + +V   +V++G+ITI
Sbjct:    6 QISYLANSVIVRDKEIESGMKVDTKFNGS--HFTIICDGKIYLTKFTNDIQVAGKEVKDGRITI 67
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BLAST of SMED30029399 vs. Planmine SMEST
Match: SMESG000015124.1 (SMESG000015124.1)

HSP 1 Score: 50.0618 bits (118), Expect = 2.724e-9
Identity = 23/29 (79.31%), Postives = 27/29 (93.10%), Query Frame = 2 
Query:   47 HITYPGNSIVVLDKAIQQDMSVSTEYDGS 133
            +ITY GNSI+VLDKAIQQDMSVST++D S
Sbjct:    6 YITYQGNSILVLDKAIQQDMSVSTKFDVS 34
The following BLAST results are available for this feature:
BLAST of SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 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 SMED30029399 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000015116.12.452e-4498.53SMESG000015116.1[more]
SMESG000015118.17.521e-1247.62SMESG000015118.1[more]
SMESG000015125.12.006e-1043.75SMESG000015125.1[more]
SMESG000015124.12.724e-979.31SMESG000015124.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029399 ID=SMED30029399|Name=SMED30029399|organism=Schmidtea mediterranea sexual|type=transcript|length=251bp
ATCCATGGAAACTTTGAAACAAATGACGCCTCAGAATGTCATTGGTCATA
TTACATACCCAGGAAATTCTATCGTTGTGCTTGACAAAGCGATTCAGCAA
GACATGAGTGTATCGACTGAATACGACGGATCTTGCAGTAGATTTGTGAT
TATTTGCGGTGACAAGACCTATAAGACTAAGTTCGATGTCAACAAGGAGG
TCACTGAAACGAAGGTAGAAAATGGAAAAATAACCATTATATGCTCTAAC
T
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx