SMED30016865

Overview
NameSMED30016865
Smed IDSMED30016865
Length (bp)2018
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 SMED30016865 (SMED30016865) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016865 (SMED30016865) 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 SMED30016865 (SMED30016865) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016865 (SMED30016865) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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




SMED30016865

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 cellSMED30016865h1SMcG0010857 SmedASXL_004864SmedAsxl_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
SMED30016865 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006838:6851..8931 +9996
Homology
The following BLAST results are available for this feature:
BLAST of SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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 SMED30016865 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

>SMED30016865 ID=SMED30016865|Name=SMED30016865|organism=Schmidtea mediterranea sexual|type=transcript|length=2018bp
TGATTTTCTATTAAACCTTTTAAAATTTTAATTGCTTTTTCGTTATTGTA
ATATTTTATTTACTTTTTCTAACAAGTTCAAATTTTTATAAATGATCGTT
TTCACAAATGCCACAAAAATTTCTCTTATCTATTAATAAAACAATAATTG
CTATGTTTGGCGTTACTTGAGATTGATGTCATTAGATCACTATTTGTCAA
ACATTCAGAACACACAGAATAAATGCAATGGAAAAGCAAGTTTGAGTAAA
GTAAACGATTTGATAAGTTACATTATATAGTAATTAAAAATTTATGCAAA
TGCTTCATCATATTTTATTTTAATGTATAATTTAAAATTCTTCAGTGTAT
TTTATTAATTAAACTAATGTGTTTTGAATCTCATAATAAAAATTAAATAA
TTCATTTTAATTAGTTTTAATCGTAAAGCAACAGTCATATAGTAATCGAA
ATGATTTTATAAGATTGCTGCTCGATATTGTAGGGTAAGTAACTTTTCTA
ATCGTGTTAAAATCTTTCATTAAATCGAATTATAGTTTTCTAACTATATT
AAATTTTAGAATTTCTATGGTTTTCCTCATTTTGTCTCAGAATCTGAGAA
ATCTACTTGTTCTTACTCTTCTATATTTTAATATTTATTTCCATCCTCTC
GACTTAAATAAGTCCATTATCGTTGATCTAACATAATTATTTTCAAACAT
TACATATTAGAACATTCTCTGTAAATTCCCATTCTCTATATCCTTGATAG
CCTGACCGAATACCATCGCGCCTCGAATTAAGATAATCCTATTGGAATAT
CAAGTATTTTTACTTTGTTTTAATTCTATTAAATTTTATGGCATTATAAA
ATTAATTGATTTCAAATGAAGTCAATATTAGGAAATAAATGTATTTATCT
GATGATTCTGCATCAACTAAAGAAAATGTTAAAAGCCACAAATGGATTTT
AACATGTTCCAAAAGACTGCCGGCCGCAGCCCTAAATATCGCATCACAGA
ATATTGAGAATTATATTAACAAAATAGCATCGCATATTAAAAGACTCTAC
GAAATTGCTGATGTTCACGAAAAAAACTTTCAACATTTATATTTTCAAAT
TTTGGACGTTTTTGAAAAAATAAATCTCATTTCAGAAGTGAATCGAATTT
CAAATATTCCACAATACGAATTCAATAATTACATTTTGATTTTGGAATAT
TTCTGGGAATCAATCTGCGAATATTATGCGGTGAAATTTTGGTTTTTCAA
TGTTTTATGCAGATCGGAATCTGTGGATTATTTTTTCAGATCAGCTTTAA
TGGAACAGGAATATCATTTGAGTCATATTTCTATTGAATTGATAGATTCC
AATACTTACTTGAGGCATATTTCCCATTATTACGATAGTTGCAATTATTG
GAGGCAACTGAATTCCAAGTTGCGATTCCTAATCATAGAAACCGGGAAAA
ATATGTTCGTCAAATTAGAGGCTCAAAGCGTCACCGTTTCAAATGTTTTA
ATAAATATAAACGATGAAGTTCTTTTAGAAAAATACCGACTTAGATCTAA
ACTTCAGCTTTTTAAATTAGAGAAATTCCTTATAATAATGTTTATTTTGT
TTTTATTACTTTTATTCCACTACTTCACGATATATTTGAATGAGGCTTAT
AATTTTCATTTTCCAAGTCTCGGTACAACTCTGATTTGCTTTTTGGGAAG
TACCGACATTATTGCCAAAACGAGTGCCTGTTGGGATCCAAAGAATTTGA
ATATTAATTTGCAAATATTTCATTTGACTTTATTATGGACTATAGTTTCA
ATAATTGTATATTGTGTTTATACTTATTTAATTTCACTTTTTGAATTGCA
GACCTTTGCAATTTTGGAAGATTATGCAAATCTTGGAGAAAAATTAAAAC
TAATAAAACACGAGTACGAATTAATGAAAAGATTTACTATCATTTCTTTG
TAATTAAATATGGATTAAAACAAAAATTTTTATTTAATATACATGTTTCA
AAAATTACTATATTTCGG
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protein sequence of SMED30016865-orf-1

>SMED30016865-orf-1 ID=SMED30016865-orf-1|Name=SMED30016865-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=355bp
MYLSDDSASTKENVKSHKWILTCSKRLPAAALNIASQNIENYINKIASHI
KRLYEIADVHEKNFQHLYFQILDVFEKINLISEVNRISNIPQYEFNNYIL
ILEYFWESICEYYAVKFWFFNVLCRSESVDYFFRSALMEQEYHLSHISIE
LIDSNTYLRHISHYYDSCNYWRQLNSKLRFLIIETGKNMFVKLEAQSVTV
SNVLININDEVLLEKYRLRSKLQLFKLEKFLIIMFILFLLLLFHYFTIYL
NEAYNFHFPSLGTTLICFLGSTDIIAKTSACWDPKNLNINLQIFHLTLLW
TIVSIIVYCVYTYLISLFELQTFAILEDYANLGEKLKLIKHEYELMKRFT
IISL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 254..276
NoneNo IPR availableTMHMMTMhelixcoord: 230..249
NoneNo IPR availableTMHMMTMhelixcoord: 296..318