SMED30021906

Overview
NameSMED30021906
Smed IDSMED30021906
Length (bp)1580
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 SMED30021906 (SMED30021906) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021906 (SMED30021906) 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




SMED30021906

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30021906SMESG000019493.1 Contig4861newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30021906SMESG000037231.1 Contig4861newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30021906SMESG000038869.1 dd_Smed_v4_1046_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30021906SMESG000038869.1 dd_Smed_v4_1046_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021906 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004252:2983..4537 +7366
v31.024981:9895..11402 -7083
Homology
The following BLAST results are available for this feature:
BLAST of SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 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 SMED30021906 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021906 ID=SMED30021906|Name=SMED30021906|organism=Schmidtea mediterranea sexual|type=transcript|length=1580bp
TTTCCGGTTCTTGTTGTTTCGACCTTACAAAATAAAAATAAATATTTTAA
AATACATTAGTAAATTGCAGTGAATTTTCAAAAGTTGCACTTTTAACAGA
TTGGCTGTCATGAATCACCCGTGATCCAAAGAAATAGTGTATCACAGTGT
CATGAGTGTTTCTCAACTCCAATATGAATATTAATGTTTTCGATTGACAT
CGGAAATATATTATATTATATATTACAAAATACGGAACACGAAATTCTTG
TGGATCTTACTTTATAATTTTTACTATAACCATGAGAAATTTTTTAATTC
TAACTTGTATTTCATCTTGAATTTTGAATGTGCTTCTTATTAATAACATT
TTCATTTTAAATGATGACATGCAATGTGTTAGTAAGGTCTAGATGTCAAA
ATAATTCTAATCCTGTCAATTGTTTGATAGCAAATGAATATAGTATGTAA
CTATACAGTATAACTTCCATAAACGTGGCTCTTCTTACTGGGGCACACTA
TAAGCGGAGCATTTGATATAAAAGGTAGTTTTAGAATATGAAGTGATGTT
AAGTATTATATGTTTAATTTTTCTTTTATAGTATATATATAATCAAATGT
CACTTTTTCTATTTTTGTCCAAATTTTTATTTTCATAATTTTCTTCATTT
CCACTATCATTTTCAATCTCTTCATCTTTGCTACCTTCATTTTCATCAAT
GGCAGTGGAAATTAAAAATGAATTAATCGATCGATCGTTATTTTATTTTA
CCGATTTAATCTAGTGCCCCCTCAGTAACAAATGCACCGGAAGTTTAGGA
GCATTTATGTGATATGGCACTGGAGAGTATCGATTTAATATTTGTAAATG
CTAATAACTCTTGCGATGAATTATTCGCGTGTCATAAATCTAACATGCTA
CTTACTCATAACCCGTTACACCATTTACACCCGGGACATTAAAATATCGC
TAGCAGACTGAATGGCTATTAGTAGCAGACCAATATCGGCAGTAAAGGAT
TACGCATAGCGGTTCTAAATGCTGGATTTAAACTATTATGCAGATACACT
GTGTAAGTGTTAAAAAAAAATCATGGAAAACGGCAATTGAGATACCAGTT
GATTTTTGATNATCTTTACGAAATGAATTTCTATTTCAACATCAGAAATC
ACTGGATATCAAATGACTGAATTTGTGACAGAGTTAATTCAAAAATTTGC
AAATATAACAAAGATACTCCGTGGTCATATCGACAATACACAAAATATAG
CTACAACTAAAACTGGTCATATTTCTATTCCGTATATATGTCGAATTGAG
CTCATTTAGGCGAGAAAACTCTTGTACTCTTGTGGTATTTACTATTTCTA
TTTGAATTTTAAGTGAAATATCATATATTTGTCAGTAAATGTAACTACAA
AATTTTGTTGTGATTTAATTGAAGTTAGCTATCATTAATTTTTTCAAAAG
TTAACTATTAAAATAGATTAATCGAGTTACCCACCACTAATATGTGTGGT
TGTTAATTAATTAAGTTTATTAATTTAAAATAATCAAAAATTTCTAATAA
CAAAACTCATGCTGAGTTTCTCAATCAGAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 32..52