SMED30014195

Overview
NameSMED30014195
Smed IDSMED30014195
Length (bp)576
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 SMED30014195 (SMED30014195) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014195 (SMED30014195) 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



SMED30014195

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
nervous systemSMED30014195h1SMcG0004881 dd_Smed_v4_62611_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014195h1SMcG0004881 dd_Smed_v4_62611_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30014195h1SMcG0004881 dd_Smed_v6_62611_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
whole organismSMED30014195h1SMcG0004881 Contig44969newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30014195h1SMcG0004881 Contig44969uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30014195 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003483:61450..62025 -2853
v31.014897:5356..5931 -2844
Homology
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BLAST of SMED30014195 vs. Planmine SMEST
Match: SMESG000060575.1 (SMESG000060575.1)

HSP 1 Score: 231.876 bits (590), Expect = 7.103e-79
Identity = 135/138 (97.83%), Postives = 135/138 (97.83%), Query Frame = -1 
Query:   61 MKYRFLNLEANLTSQYFYTPQKYFPEDGIQTGLILISVLLVCFGYLVYKSKCKRSRDIYQEEMIKRSQFDQMPIWDWSCXXXXXXXXXXXXXXXXXXXXXLSDPNVCRKQFICWLDHSRSQFCAIGHLSFSDVAINRM 474
            MKYRFLNLEANLTS YFYTPQKYFPEDGIQTGLILISVLLVCFGYLVYKSKCKRSRDIYQEEMIKRSQFDQMPIWDWSCK LKYRKRKYLNKKFKYLLPPLSDPNVCRKQFICWLDHSRSQFCAIG LSFSDVAINRM
Sbjct:    1 MKYRFLNLEANLTSPYFYTPQKYFPEDGIQTGLILISVLLVCFGYLVYKSKCKRSRDIYQEEMIKRSQFDQMPIWDWSCKLLKYRKRKYLNKKFKYLLPPLSDPNVCRKQFICWLDHSRSQFCAIGQLSFSDVAINRM 138
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BLAST of SMED30014195 vs. Planmine SMEST
Match: SMESG000059770.1 (SMESG000059770.1)

HSP 1 Score: 60.077 bits (144), Expect = 4.067e-11
Identity = 26/52 (50.00%), Postives = 39/52 (75.00%), Query Frame = -1 
Query:  241 DGIQTGLILISVLLVCFGYLVYKSKCKRSRDIYQEEMIKRSQFDQMPIWDWS 396
            DGIQTG++L+++L+  F Y +++SKCKR   IY++E+IKRS+ D     DWS
Sbjct:   61 DGIQTGIVLMAILVFIFIYGIFRSKCKREGQIYEKELIKRSRQDPFKPHDWS 112
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BLAST of SMED30014195 vs. Planmine SMEST
Match: SMESG000012741.1 (SMESG000012741.1)

HSP 1 Score: 47.3654 bits (111), Expect = 1.115e-6
Identity = 29/56 (51.79%), Postives = 42/56 (75.00%), Query Frame = -1 
Query:  241 YFPEDGIQTGLILISVLLVCFGYLVYKSKCKRSRDIYQEEMIKRSQFDQMPIWDWS 408
            Y P +GIQTG++L SVLLV F Y + K+KCKR  ++Y++EMI++S+ D   +WD S
Sbjct:   50 YSPNEGIQTGVVLGSVLLVVFLYGIIKAKCKRKSELYEKEMIRKSRNDPHKMWDLS 105
The following BLAST results are available for this feature:
BLAST of SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 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 SMED30014195 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000060575.17.103e-7997.83SMESG000060575.1[more]
SMESG000059770.14.067e-1150.00SMESG000059770.1[more]
SMESG000012741.11.115e-651.79SMESG000012741.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014195 ID=SMED30014195|Name=SMED30014195|organism=Schmidtea mediterranea sexual|type=transcript|length=576bp
GAAAAGTGGAAAATATTCCATTATTCTTAGAATAATTGAAAAAGATATTT
ATATGGAAAACATCCGATTTATCGCAACATCTGAAAAACTCAAATGGCCG
ATTGCGCAAAATTGAGATCTCGAGTGATCCAGCCAGCATATAAATTGTTT
CCTACAGACATTCGGATCAGATAATGGCGGCAATAAATACTTGAATTTCT
TGTTCAAATATTTCCTTTTTCGGTATTTCAGTTGTTTACATGACCAATCC
CAAATTGGCATCTGATCGAATTGGGATCTTTTGATCATTTCTTCCTGGTA
AATGTCTCGAGATCTTTTGCATTTCGATTTGTAAACCAAATATCCAAAAC
ACACCAGAAGAACGGAAATCAAAATTAATCCAGTTTGAATCCCATCTTCC
GGGAAATATTTTTGAGGCGTATAAAAATACTGAGAAGTCAAATTGGCTTC
CAAATTCAAGAAACGATATTTCATAATTCCATTGAAAATGAGAACAATTT
GAATTTTATATTTTTCTTATCTCAATTTTGCTGATTTTCAATTTTGTTTT
TTATTAGCCAATAAAATTCTTGATAA
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protein sequence of SMED30014195-orf-1

>SMED30014195-orf-1 ID=SMED30014195-orf-1|Name=SMED30014195-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=142bp
MKYRFLNLEANLTSQYFYTPQKYFPEDGIQTGLILISVLLVCFGYLVYKS
KCKRSRDIYQEEMIKRSQFDQMPIWDWSCKQLKYRKRKYLNKKFKYLLPP
LSDPNVCRKQFICWLDHSRSQFCAIGHLSFSDVAINRMFSI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000136whole organism
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 29..48