SMED30034198

Overview
NameSMED30034198
Smed IDSMED30034198
Length (bp)280
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30034198

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30034198h1SMcG0010524 SmedASXL_016974SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30034198h1SMcG0010524 dd_Smed_v4_12484_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30034198h1SMcG0010524 dd_Smed_v4_12484_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30034198h1SMcG0010524 dd_Smed_v4_12484_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
non-ciliated neuronSMED30034198h1SMcG0010524 dd_Smed_v4_12484_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30034198h1SMcG0010524 dd_Smed_v6_12484_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30034198 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000798:91875..92257 -1326
Homology
[Close]
BLAST of SMED30034198 vs. TrEMBL
Match: H6WA41 (SFI1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 193.356 bits (490), Expect = 3.795e-56
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = -3 
Query:    3 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 278
            EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL
Sbjct:  226 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 317
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BLAST of SMED30034198 vs. Planmine SMEST
Match: SMESG000002829.1 (SMESG000002829.1)

HSP 1 Score: 197.978 bits (502), Expect = 2.546e-60
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = -3 
Query:    3 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 278
            EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL
Sbjct:  308 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 399
[Close]
BLAST of SMED30034198 vs. Planmine SMEST
Match: SMESG000002829.1 (SMESG000002829.1)

HSP 1 Score: 197.978 bits (502), Expect = 2.621e-60
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = -3 
Query:    3 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 278
            EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL
Sbjct:  308 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 399
[Close]
BLAST of SMED30034198 vs. Planmine SMEST
Match: SMESG000002829.1 (SMESG000002829.1)

HSP 1 Score: 197.978 bits (502), Expect = 3.032e-60
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = -3 
Query:    3 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 278
            EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL
Sbjct:  329 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 420
[Close]
BLAST of SMED30034198 vs. Planmine SMEST
Match: SMESG000002829.1 (SMESG000002829.1)

HSP 1 Score: 197.978 bits (502), Expect = 3.183e-60
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = -3 
Query:    3 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 278
            EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL
Sbjct:  329 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 420
[Close]
BLAST of SMED30034198 vs. Planmine SMEST
Match: SMESG000002829.1 (SMESG000002829.1)

HSP 1 Score: 195.667 bits (496), Expect = 1.937e-59
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = -3 
Query:    3 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 278
            EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL
Sbjct:  329 EKERWDSHYNWNLAHRYLMKWKQHHAHLLVEYAMADRCQEMRRRFQLRKYFIQWQKYYGEEKVLRVQQKLADQMNEILIKRRVWCHFKSFIL 420
The following BLAST results are available for this feature:
BLAST of SMED30034198 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 SMED30034198 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 SMED30034198 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 SMED30034198 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 SMED30034198 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 SMED30034198 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 SMED30034198 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 SMED30034198 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
H6WA413.795e-56100.00SFI1 (Fragment) OS=Schmidtea mediterranea OX=79327... [more]
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BLAST of SMED30034198 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 SMED30034198 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 SMED30034198 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 SMED30034198 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 SMED30034198 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 SMED30034198 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000002829.12.546e-60100.00SMESG000002829.1[more]
SMESG000002829.12.621e-60100.00SMESG000002829.1[more]
SMESG000002829.13.032e-60100.00SMESG000002829.1[more]
SMESG000002829.13.183e-60100.00SMESG000002829.1[more]
SMESG000002829.11.937e-59100.00SMESG000002829.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034198 ID=SMED30034198|Name=SMED30034198|organism=Schmidtea mediterranea sexual|type=transcript|length=280bp
TGCAAAATGAAGGATTTGAAGTGACACCAGACTCGTCTCTTGATCAGAAT
CTCATTCATCTGATCAGCCAATTTCTGTTGGACTCTCAGAACCTTTTCCT
CTCCATAATATTTCTGCCATTGAATGAAATATTTTCTCAGTTGAAATCTC
CTGCGCATTTCCTGGCATCTGTCCGCCATAGCATACTCGACCAATAGATG
TGCGTGATGCTGTTTCCATTTCATCAAATATCTGTGGGCCAAATTCCAAT
TGTAATGACTATCCCACCGTTCCTTTTCCT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
PLANA:0000418head