meis

Overview
Namemeis (AFP48375.1)
Smed IDSMED30035599
Length (bp)588
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ 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




 

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 meis (SMED30035599) t-SNE clustered cells

Violin plots show distribution of expression levels for meis (SMED30035599) in cells (dots) of each of the 12 neoblast clusters.

 

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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 meis (SMED30035599) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for meis (SMED30035599) 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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Homology
BLAST of meis vs. TrEMBL
Match: J7FUV3 (Meis OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 248.054 bits (632), Expect = 4.947e-76
Identity = 139/139 (100.00%), Postives = 139/139 (100.00%), Query Frame = 2
Query:  131 GFTPELYSAAHGSSLGMPVXXXXXXXXYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQXXXXXXXIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGLSSFSHQNHVGRLDSNNSKTGHSL 547
            GFTPELYSAAHGSSLGMPVAAAAAAAAYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQAAAAAAAIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGLSSFSHQNHVGRLDSNNSKTGHSL
Sbjct:  144 GFTPELYSAAHGSSLGMPVAAAAAAAAYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQAAAAAAAIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGLSSFSHQNHVGRLDSNNSKTGHSL 282          
BLAST of meis vs. Planmine SMEST
Match: SMESG000006530.1 (SMESG000006530.1)

HSP 1 Score: 259.61 bits (662), Expect = 1.196e-82
Identity = 144/144 (100.00%), Postives = 144/144 (100.00%), Query Frame = 2
Query:  131 GFTPELYSAAHGSSLGMPVXXXXXXXXYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQXXXXXXXIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGLSSFSHQNHVGRLDSNNSKTGHSLQDIHV 562
            GFTPELYSAAHGSSLGMPVAAAAAAAAYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQAAAAAAAIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGLSSFSHQNHVGRLDSNNSKTGHSLQDIHV
Sbjct:  581 GFTPELYSAAHGSSLGMPVAAAAAAAAYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQAAAAAAAIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGLSSFSHQNHVGRLDSNNSKTGHSLQDIHV 724          
BLAST of meis vs. Planmine SMEST
Match: SMESG000006530.1 (SMESG000006530.1)

HSP 1 Score: 254.603 bits (649), Expect = 8.465e-81
Identity = 142/142 (100.00%), Postives = 142/142 (100.00%), Query Frame = 2
Query:  137 TPELYSAAHGSSLGMPVXXXXXXXXYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQXXXXXXXIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGLSSFSHQNHVGRLDSNNSKTGHSLQDIHV 562
            TPELYSAAHGSSLGMPVAAAAAAAAYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQAAAAAAAIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGLSSFSHQNHVGRLDSNNSKTGHSLQDIHV
Sbjct:  579 TPELYSAAHGSSLGMPVAAAAAAAAYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQAAAAAAAIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGLSSFSHQNHVGRLDSNNSKTGHSLQDIHV 720          
The following BLAST results are available for this feature:
BLAST of meis 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 meis 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 meis 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 meis 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 meis 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 meis 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 meis 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 meis vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
J7FUV34.947e-76100.00Meis OS=Schmidtea mediterranea OX=79327 PE=2 SV=1[more]
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BLAST of meis 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 meis 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 meis 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 meis 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 meis 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 meis vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000006530.11.196e-82100.00SMESG000006530.1[more]
SMESG000006530.18.465e-81100.00SMESG000006530.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30035599
GenBankAFP48375.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035599 ID=SMED30035599|Name=meis|organism=Schmidtea mediterranea sexual|type=transcript|length=588bp
GCCTAATTGCCTATCAGCAGATATGAAAACATTCAATGTTAGTAGTTCAG
TTATTAAGAGCAGTACTTCAGTCTTTTTGACTTATATCCTTTCACCGTGA
AATTGATGTGACTTATGCCTCACTGTTACCGGTTTCACTCCAGAACTGTA
TTCTGCTGCTCATGGAAGTTCTCTTGGAATGCCAGTAGCAGCGGCAGCCG
CAGCAGCCGCGTATCAAAATATGAGCGCGGCTCAATACATGACAGCCGGC
CAACAAGCGGCAATGCTTCATCAACAAGCAGCCATAATGGGAGGTCACCC
AAGTTACATTCAAGCGGCGGCCGCAGCAGCTGCTATTGGGTATAGCAACA
CTCCAGTTTCGTATTCACATTCATCATTGCATCAATATCACGTGTTTCCG
AATAATAACTCACCGCCACTGAGCTCAGGGGCCTCAAATAATTTCAATCA
ACATTATAATAATTTACAAGCTGGATTATCATCATTTTCACATCAGAATC
ACGTCGGCCGCCTAGATTCTAATAATTCGAAAACTGGACATTCCCTGCAA
GATATTCATGTTTGAATGTCTGCCAGCTGTAATTATGT
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protein sequence of SMED30035599-orf-1

>SMED30035599-orf-1 ID=SMED30035599-orf-1|Name=SMED30035599-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=129bp
MPVAAAAAAAAYQNMSAAQYMTAGQQAAMLHQQAAIMGGHPSYIQAAAAA
AAIGYSNTPVSYSHSSLHQYHVFPNNNSPPLSSGASNNFNQHYNNLQAGL
SSFSHQNHVGRLDSNNSKTGHSLQDIHV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000017photoreceptor neuron
PLANA:0000099neuron
PLANA:0000103central nervous system
PLANA:0003104enteric muscle cell
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
Vocabulary: biological process
TermDefinition
GO:0006355regulation of transcription, DNA-templated