SMED30031322

Overview
NameSMED30031322
Smed IDSMED30031322
Length (bp)376
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 SMED30031322 (SMED30031322) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031322 (SMED30031322) 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



SMED30031322

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
copulatory apparatusSMED30031322h1SMcG0005118 PL05009A1C01smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
reproductive organSMED30031322h1SMcG0005118 Contig51663newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031322h1SMcG0005118 Contig51663uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30031322 vs. Planmine SMEST
Match: SMESG000053385.1 (SMESG000053385.1)

HSP 1 Score: 92.4337 bits (228), Expect = 5.030e-25
Identity = 124/125 (99.20%), Postives = 124/125 (99.20%), Query Frame = 2 
Query:    2 AIQTFMICLSLSIISLNAKPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAERXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEGTGWNSFRLRSLASNAYIVIPGNIDTFGRPIKI 376
            AIQTFMICLSLSIISLNAKPSGYGGIGHSGGVISEVGHSGFDS FGGNGGIFGGSVGAERGDFGVGDGFGGSSGLTGSIGGVIGAGVASGLEGTGWNSFRLRSLASNAYIVIPGNIDTFGRPIKI
Sbjct:    2 AIQTFMICLSLSIISLNAKPSGYGGIGHSGGVISEVGHSGFDSGFGGNGGIFGGSVGAERGDFGVGDGFGGSSGLTGSIGGVIGAGVASGLEGTGWNSFRLRSLASNAYIVIPGNIDTFGRPIKI 126
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BLAST of SMED30031322 vs. Planmine SMEST
Match: SMESG000053389.1 (SMESG000053389.1)

HSP 1 Score: 88.5817 bits (218), Expect = 1.657e-23
Identity = 120/125 (96.00%), Postives = 121/125 (96.80%), Query Frame = 2 
Query:    2 AIQTFMICLSLSIISLNAKPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAERXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEGTGWNSFRLRSLASNAYIVIPGNIDTFGRPIKI 376
            +IQTFMICLSLSIISLNAKPSGYGGIGHSGGVISEVGHSGFDS F GNGGIFGGSVGAE GDFGVGDGFGGSSGLTGSI GVIGAGVASGLEGTGWNSFRLRSLASNAYIVIPGNIDTFGRPIKI
Sbjct:    2 SIQTFMICLSLSIISLNAKPSGYGGIGHSGGVISEVGHSGFDSGFVGNGGIFGGSVGAEGGDFGVGDGFGGSSGLTGSIDGVIGAGVASGLEGTGWNSFRLRSLASNAYIVIPGNIDTFGRPIKI 126
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BLAST of SMED30031322 vs. Planmine SMEST
Match: SMESG000053386.1 (SMESG000053386.1)

HSP 1 Score: 61.6178 bits (148), Expect = 3.853e-13
Identity = 28/34 (82.35%), Postives = 31/34 (91.18%), Query Frame = 2 
Query:  275 EGTGWNSFRLRSLASNAYIVIPGNIDTFGRPIKI 376
            EGTGWNSFRLRSL+SNA +VIPGNI+TFGR  KI
Sbjct:   83 EGTGWNSFRLRSLSSNAQLVIPGNINTFGRRFKI 116

HSP 2 Score: 43.1282 bits (100), Expect = 5.221e-6
Identity = 20/20 (100.00%), Postives = 20/20 (100.00%), Query Frame = 2 
Query:    2 AIQTFMICLSLSIISLNAKP 61
            AIQTFMICLSLSIISLNAKP
Sbjct:    2 AIQTFMICLSLSIISLNAKP 21
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BLAST of SMED30031322 vs. Planmine SMEST
Match: SMESG000053313.1 (SMESG000053313.1)

HSP 1 Score: 51.9878 bits (123), Expect = 2.096e-9
Identity = 24/32 (75.00%), Postives = 27/32 (84.38%), Query Frame = 2 
Query:  281 TGWNSFRLRSLASNAYIVIPGNIDTFGRPIKI 376
            TGWNSF LRSL++NAYIVIPGN+ TF R  KI
Sbjct:   95 TGWNSFTLRSLSNNAYIVIPGNLKTFRRRYKI 126

HSP 2 Score: 42.743 bits (99), Expect = 8.779e-6
Identity = 20/20 (100.00%), Postives = 20/20 (100.00%), Query Frame = 2 
Query:    2 AIQTFMICLSLSIISLNAKP 61
            AIQTFMICLSLSIISLNAKP
Sbjct:    2 AIQTFMICLSLSIISLNAKP 21
[Close]
BLAST of SMED30031322 vs. Planmine SMEST
Match: SMESG000053358.1 (SMESG000053358.1)

HSP 1 Score: 51.6026 bits (122), Expect = 3.624e-9
Identity = 24/33 (72.73%), Postives = 27/33 (81.82%), Query Frame = 2 
Query:  278 GTGWNSFRLRSLASNAYIVIPGNIDTFGRPIKI 376
            G  WNSFRLRSL++NAYIVIPGN+ TF R  KI
Sbjct:   94 GIEWNSFRLRSLSNNAYIVIPGNLKTFRRRYKI 126
The following BLAST results are available for this feature:
BLAST of SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 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 SMED30031322 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000053385.15.030e-2599.20SMESG000053385.1[more]
SMESG000053389.11.657e-2396.00SMESG000053389.1[more]
SMESG000053386.13.853e-1382.35SMESG000053386.1[more]
SMESG000053313.12.096e-975.00SMESG000053313.1[more]
SMESG000053358.13.624e-972.73SMESG000053358.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031322 ID=SMED30031322|Name=SMED30031322|organism=Schmidtea mediterranea sexual|type=transcript|length=376bp
GGCTATTCAAACCTTCATGATATGTTTATCATTATCAATAATTTCACTGA
ATGCAAAACCAAGCGGATACGGAGGCATTGGTCATTCAGGAGGTGTGATA
TCAGAGGTCGGTCATTCAGGCTTTGATTCTGATTTCGGTGGAAATGGAGG
GATTTTTGGTGGCTCTGTTGGAGCCGAAAGAGGAGATTTTGGGGTTGGCG
ACGGCTTCGGTGGTTCTTCCGGACTTACTGGAAGTATTGGTGGTGTAATA
GGAGCAGGTGTTGCATCTGGATTAGAAGGAACAGGATGGAATTCGTTTAG
ATTAAGAAGTCTAGCGTCAAATGCTTATATAGTCATTCCTGGAAATATTG
ATACATTCGGAAGACCAATTAAAATA
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protein sequence of SMED30031322-orf-1

>SMED30031322-orf-1 ID=SMED30031322-orf-1|Name=SMED30031322-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
AIQTFMICLSLSIISLNAKPSGYGGIGHSGGVISEVGHSGFDSDFGGNGG
IFGGSVGAERGDFGVGDGFGGSSGLTGSIGGVIGAGVASGLEGTGWNSFR
LRSLASNAYIVIPGNIDTFGRPIKI
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000232copulatory apparatus
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.491