SMED30015223

Overview
NameSMED30015223
Smed IDSMED30015223
Length (bp)841
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30015223 (SMED30015223) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015223 (SMED30015223) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30015223

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
X1 cellSMED30015223h1SMcG0012181 SmedASXL_077184SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30015223 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009190:24995..25792 +2049
Homology
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BLAST of SMED30015223 vs. Planmine SMEST
Match: SMESG000030694.1 (SMESG000030694.1)

HSP 1 Score: 169.859 bits (429), Expect = 1.952e-47
Identity = 95/165 (57.58%), Postives = 113/165 (68.48%), Query Frame = 3 
Query:   63 HILQGCWRTHGMRVERHNNICRRIKTIMRAKDSEVIEEPRLQTNEVSENLTY*FAIKEKIIICDAQLVADSAKIKER*NSTRKIQ**QKQGNLS---------DESTRTLKLWL*HSNEEGAISKDSMRDLDVLLEIKAKEITKMSKKILRDNSIMVMMHRNRTE 530
            HILQGCWRTHGMRVERHNNICRRIK IM+ K+SEV+EEPRLQTNE           K KIIICDAQ+VADS+       + RKI   +K   ++         DE    + +     N  GAISK S+RDLD+LL+IK+KE+ KMS+KI+RDNSIMV MHRNRTE
Sbjct:  837 HILQGCWRTHGMRVERHNNICRRIKAIMKGKESEVVEEPRLQTNEGLRKPDLLICHKGKIIICDAQVVADSSNCSLESENQRKIDYYKKDSVVAEARKLIGRDDEDIIIMAVTF---NWRGAISKTSIRDLDMLLDIKSKEVIKMSRKIIRDNSIMVEMHRNRTE 998
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BLAST of SMED30015223 vs. Planmine SMEST
Match: SMESG000064503.1 (SMESG000064503.1)

HSP 1 Score: 80.8777 bits (198), Expect = 6.327e-27
Identity = 38/48 (79.17%), Postives = 45/48 (93.75%), Query Frame = 3 
Query:  387 NEEGAISKDSMRDLDVLLEIKAKEITKMSKKILRDNSIMVMMHRNRTE 530
            N  GAI+KDSMRDL++LL+IK+KE+ KMS+KILRDNSIMVMMHRNRTE
Sbjct:  258 NWRGAIAKDSMRDLEILLDIKSKEVIKMSRKILRDNSIMVMMHRNRTE 305

HSP 2 Score: 58.5362 bits (140), Expect = 6.327e-27
Identity = 27/41 (65.85%), Postives = 33/41 (80.49%), Query Frame = 2 
Query:  278 ENKRKIE*YKKDSVVTEARKLIGRIDENIEVMAVTFKRRGS 400
            ENKRKI+ YKKDS++ E RKLIGR++ENI  MA TF  RG+
Sbjct:  222 ENKRKIDYYKKDSIIKETRKLIGRVEENIIAMAFTFNWRGA 262
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BLAST of SMED30015223 vs. Planmine SMEST
Match: SMESG000019752.1 (SMESG000019752.1)

HSP 1 Score: 105.916 bits (263), Expect = 1.577e-25
Identity = 62/127 (48.82%), Postives = 78/127 (61.42%), Query Frame = 3 
Query:   63 HILQGCWRTHGMRVERHNNICRRIKTIMRAKDSEVIEEPRLQTNEVSENLTY*FAIKEKIIICDAQLVADSAKIKER*NSTRKIQ**QKQ------GNLSDESTRTLKLWL*HSNEEGAISKDSMRD 425
            HILQGCWRTHGMRVERH+NIC RIK+IM+ K SE+IE+PRLQT++           K+K+IICDAQ+VADS+       + RKI   +K       G L       + +     N  GAISK +MRD
Sbjct:  426 HILQGCWRTHGMRVERHDNICHRIKSIMKLKGSELIEKPRLQTDKGLRKPDLLIRHKDKVIICDAQVVADSSNCCLESENQRKIDYYKKDSVVKAAGKLIGRDDEDIIIMAVTFNWRGAISKTTMRD 552
The following BLAST results are available for this feature:
BLAST of SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 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 SMED30015223 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000030694.11.952e-4757.58SMESG000030694.1[more]
SMESG000064503.16.327e-2779.17SMESG000064503.1[more]
SMESG000019752.11.577e-2548.82SMESG000019752.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015223 ID=SMED30015223|Name=SMED30015223|organism=Schmidtea mediterranea sexual|type=transcript|length=841bp
TAAATAACATGAAAATTTATTGTTTGATGAAATGTCAGATTTATTGTGTG
ACAGACGTGTGACACATACTGCAAGGATGTTGGAGAACACATGGTATGCG
AGTAGAAAGACACAATAATATATGCCGCAGAATAAAAACCATAATGAGAG
CAAAAGATAGTGAAGTAATCGAAGAACCAAGATTACAAACGAATGAGGTC
TCAGAAAACCTGACTTACTAATTCGCCATAAAAGAAAAAATAATAATATG
TGATGCGCAATTAGTGGCAGATAGTGCGAAAATAAAAGAAAGATAGAATA
GTACAAGAAAGATTCAGTAGTAACAGAAGCAAGGAAACTTATCGGACGAA
TCGACGAGAACATTGAAGTTATGGCTGTGACATTCAAACGAAGAGGGAGC
CATTTCGAAAGACTCCATGAGAGATCTTGATGTACTGCTAGAAATAAAAG
CAAAGGAAATAACAAAGATGTCCAAAAAGATACTAAGGGACAACAGCATC
ATGGTGATGATGCATAGAAACCGAACGGAATCTGAGGGGGCATTATTATT
ATTATGGGAATGTAGCTGGGACTAACTGACATGTCTGACGATGGCCCTAA
CTCTCCTGTCCTGTATGCATTACCCCGCTAGTCCTCCTATTTCTACTGGC
CCCAACAAATTCACCATCACCACATCCGTTACCAATTACTCATAAATATC
GACCCCAAAACTGGATAAAAATCACACGGTCAAATGCCACCAGATACTTG
TTCTACCGTTATTAATTCAAAGGTAAAACGTGCGGTCCCAATGTGCCTTA
TATCTCGGCACCAGGCCCGTTAAAATGCGCTCAAATTCCGA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: molecular function
TermDefinition
GO:0003964RNA-directed DNA polymerase activity
Vocabulary: biological process
TermDefinition
GO:0006278RNA-dependent DNA biosynthetic process
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 37..59
NoneNo IPR availableTMHMMTMhelixcoord: 5..27