SMED30018040

Overview
NameSMED30018040
Smed IDSMED30018040
Length (bp)291
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 SMED30018040 (SMED30018040) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018040 (SMED30018040) 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



SMED30018040

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
prepharyngeal regionSMED30018040SMESG000062648.1 SmedASXL_078948SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
gutSMED30018040SMESG000062648.1 dd_Smed_v4_314_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30018040SMESG000062648.1 dd_Smed_v6_314_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
goblet cellSMED30018040SMESG000062648.1 dd_Smed_v6_314_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018040 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002111:32226..32493 +1340
Homology
[Close]
BLAST of SMED30018040 vs. Planmine SMEST
Match: SMESG000062648.1 (SMESG000062648.1)

HSP 1 Score: 124.02 bits (310), Expect = 1.515e-38
Identity = 62/69 (89.86%), Postives = 66/69 (95.65%), Query Frame = 3 
Query:   15 IDANNIF-L*ICLLFINSWMVPDIEASKCHDNCRNNYNTCIRACNLRKPPSRNCFSDCIRYNTNCLLFC 218
            +++N +F L ICLLFINSWMVPDIEASKCHDNCRNNYNTCIRACNLRKPPSRNCFSDCIRYNTNCLLFC
Sbjct:   13 VNSNKMFALLICLLFINSWMVPDIEASKCHDNCRNNYNTCIRACNLRKPPSRNCFSDCIRYNTNCLLFC 81
[Close]
BLAST of SMED30018040 vs. Planmine SMEST
Match: SMESG000062670.1 (SMESG000062670.1)

HSP 1 Score: 41.2022 bits (95), Expect = 3.962e-6
Identity = 25/66 (37.88%), Postives = 35/66 (53.03%), Query Frame = 3 
Query:   30 IFL*ICLLFINSWMVPDIEASKCHDNCRNNYNTCIRACNLRKPPSRNCFSDCIRYNTNCLLFC*KF 227
            I L IC+L IN+  + D EA+KC D C      CI +C+        C  +C +Y+  CL FC K+
Sbjct:    2 ISLLICVLLINAIYIADSEATKCQDKCAKAKAYCIHSCDSSSLSKSKCLRNCDKYHETCLKFCDKY 67
The following BLAST results are available for this feature:
BLAST of SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 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 SMED30018040 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000062648.11.515e-3889.86SMESG000062648.1[more]
SMESG000062670.13.962e-637.88SMESG000062670.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018040 ID=SMED30018040|Name=SMED30018040|organism=Schmidtea mediterranea sexual|type=transcript|length=291bp
GATTTGTTTACTCAATTGATGCGAATAATATATTTTTGTAGATTTGTTTA
CTTTTTATCAATTCTTGGATGGTTCCGGATATCGAGGCAAGCAAGTGCCA
TGATAATTGTAGAAATAACTATAATACTTGCATTAGAGCATGCAATTTGA
GGAAACCCCCAAGTCGAAACTGTTTCTCAGATTGTATAAGATATAATACC
AATTGTTTACTGTTTTGTTAAAAATTCAGCAATTTAATGTTGATTTTAAA
ATAAAATTATTATTTTAAAAAAAAAAAAAAAAAAAATGCGA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000067goblet cell
PLANA:0000419prepharyngeal region
PLANA:0000420parapharyngeal region