SMED30028306

Overview
NameSMED30028306
Smed IDSMED30028306
Length (bp)854
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 SMED30028306 (SMED30028306) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028306 (SMED30028306) 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



SMED30028306

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 4 cellSMED30028306SMESG000056142.1 dd_Smed_v4_12968_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
SMED30028306 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007571:2610..3463 -4252
Homology
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BLAST of SMED30028306 vs. Planmine SMEST
Match: SMESG000056075.1 (SMESG000056075.1)

HSP 1 Score: 55.4546 bits (132), Expect = 4.051e-9
Identity = 46/145 (31.72%), Postives = 76/145 (52.41%), Query Frame = 1 
Query:  286 KQHPIKLKTHVFNVIISACLTIEGCLIIGFTISDALNAQHFTHNSIYRFSVXXXXXXXXXXXXXXXXXXXXXXFN---SKYLLIFLLGIESGCFLSLLYVSGILFEQMIVNLSIDYYPKIMFEKFCFSMICVFSLLFHLVVALRY 711
            +++ I  KT V NV++S  L + G   IGF I   +      + ++Y  S ++   ++ I+  ++G      K N   SKYL++F + +E GC    L V+   F+Q I+N S  +Y KI+   F  SM    +L+FHL++  RY
Sbjct:   49 ERNQISSKTQVLNVVLSVILIVMGIFTIGFLIYGII---FLRYAAVYYISHLVFSFLIGILLIAVGACGIRMKLNKTYSKYLVLFTIAVEGGCLFIFLLVAANTFQQ-IMNDSYSFYRKIITGLFGVSMFSALNLIFHLIIVARY 189
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BLAST of SMED30028306 vs. Planmine SMEST
Match: SMESG000056059.1 (SMESG000056059.1)

HSP 1 Score: 55.0694 bits (131), Expect = 5.958e-9
Identity = 46/145 (31.72%), Postives = 76/145 (52.41%), Query Frame = 1 
Query:  286 KQHPIKLKTHVFNVIISACLTIEGCLIIGFTISDALNAQHFTHNSIYRFSVXXXXXXXXXXXXXXXXXXXXXXFN---SKYLLIFLLGIESGCFLSLLYVSGILFEQMIVNLSIDYYPKIMFEKFCFSMICVFSLLFHLVVALRY 711
            +++ I  KT V NV++S  L + G   IGF I   +      + ++Y  S ++   ++ I+  ++G      K N   SKYL++F + +E GC    L V+   F+Q I+N S  +Y KI+   F  SM    +L+FHL++  RY
Sbjct:   49 ERNQISSKTQVLNVVLSVILIVMGIFTIGFLIYGII---LLRYAAVYYISHLVFSFLIGILLIAVGACGIRMKLNKTYSKYLVLFTIAVEGGCLFIFLLVAANTFQQ-IMNDSYSFYRKIITGLFGVSMFSALNLIFHLIIVARY 189
The following BLAST results are available for this feature:
BLAST of SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 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 SMED30028306 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000056075.14.051e-931.72SMESG000056075.1[more]
SMESG000056059.15.958e-931.72SMESG000056059.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028306 ID=SMED30028306|Name=SMED30028306|organism=Schmidtea mediterranea sexual|type=transcript|length=854bp
TATTCACAAAACCATTCAACGACATTAAAAAGATAATAATTGTGTTTGAC
TGTGTGCTAGATTATCTCGTCTATTGTAGAATATTTTTAACAATTACTTT
GATATTTTAACCATTTTTAATTGAATGCTTTCAAAATTCACTTGAATACT
TAGCAACATAAAGAAATTGGAGATTTTGCATTTTTTAAAAGCATGAATTA
TTTGAAGTCAATTGGTGGAAATTTCCAATTAGAAAATCATAATTTCATTG
GATCTAGGATAAAAAGCACAGCGGTTGAAAATCTAAAACAACATCCAATC
AAATTAAAGACGCATGTTTTTAACGTCATCATTAGCGCATGTTTAACAAT
TGAAGGATGTTTAATTATTGGATTTACTATTTCAGACGCGTTAAATGCCC
AACATTTTACTCACAATTCAATTTATCGTTTTTCAGTAATAATATTAATT
GGAATCTTATTAATAATTTCTGGTTCAATTGGAATAAAAATGAAGTTGAG
TAAATTTAATAGCAAATATTTGTTAATTTTTCTGCTTGGTATTGAAAGCG
GATGTTTCTTAAGTTTATTATATGTTAGCGGAATTTTATTTGAGCAAATG
ATAGTCAACTTGTCAATAGATTATTATCCAAAAATTATGTTTGAAAAATT
TTGCTTTTCAATGATATGCGTATTTTCTCTATTATTTCATTTAGTAGTCG
CCTTACGGTATGGTGAAAATTTGATTAAAACTGTTGAAAAATAAATTAAG
TTTTTATCTCTATGTACATTTATTCGGTTTGGTTATCAGAACATATTAAA
TGTATATATATTTCTTTATATGGCTTCATATTAAAGTTATATAAATTTTG
TTTT
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protein sequence of SMED30028306-orf-1

>SMED30028306-orf-1 ID=SMED30028306-orf-1|Name=SMED30028306-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=184bp
MNYLKSIGGNFQLENHNFIGSRIKSTAVENLKQHPIKLKTHVFNVIISAC
LTIEGCLIIGFTISDALNAQHFTHNSIYRFSVIILIGILLIISGSIGIKM
KLSKFNSKYLLIFLLGIESGCFLSLLYVSGILFEQMIVNLSIDYYPKIMF
EKFCFSMICVFSLLFHLVVALRYGENLIKTVEK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 76..98
NoneNo IPR availableTMHMMTMhelixcoord: 41..63
NoneNo IPR availableTMHMMTMhelixcoord: 148..170
NoneNo IPR availableTMHMMTMhelixcoord: 111..133