SMED30029158

Overview
NameSMED30029158
Smed IDSMED30029158
Length (bp)442
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



SMED30029158

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30029158h1SMcG0016099 Contig6015newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30029158h1SMcG0016099 Contig6015uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
X1 cellSMED30029158h1SMcG0016099 SmedASXL_014832SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30029158h1SMcG0016099 SmedASXL_014832SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30029158h1SMcG0016099 SmedASXL_025037SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30029158h1SMcG0016099 SmedASXL_014833SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30029158h1SMcG0016099 SmedASXL_014833SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30029158h1SMcG0016099 dd_Smed_v4_9264_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029158h1SMcG0016099 dd_Smed_v4_9264_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30029158h1SMcG0016099 dd_Smed_v4_9264_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30029158 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002855:30224..30665 -2210
Homology
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BLAST of SMED30029158 vs. Planmine SMEST
Match: SMESG000033246.1 (SMESG000033246.1)

HSP 1 Score: 46.595 bits (109), Expect = 1.351e-12
Identity = 24/40 (60.00%), Postives = 26/40 (65.00%), Query Frame = -3 
Query:   45 CPNVK*LHCHKARHFS----TNAEKWRDVLENDQKYARAK 152
            CPNVK  HCHKA HF        EKW +V ENDQ+Y RAK
Sbjct:  168 CPNVKCHHCHKAEHFKHRCFQRTEKWIEVRENDQEYKRAK 207

HSP 2 Score: 42.3578 bits (98), Expect = 1.351e-12
Identity = 19/37 (51.35%), Postives = 26/37 (70.27%), Query Frame = -1 
Query:  155 RKTKEYPKKQYYFIKQIMQSNNLPKFKCCTCFEECYQ 265
            R+ +E+ KKQ  F  +I+Q NN PKFKC  CFEE ++
Sbjct:  128 RQNREHLKKQQNFNNKIVQRNNQPKFKCWVCFEEGHR 164
[Close]
BLAST of SMED30029158 vs. Planmine SMEST
Match: SMESG000027262.1 (SMESG000027262.1)

HSP 1 Score: 41.2022 bits (95), Expect = 1.473e-9
Identity = 23/40 (57.50%), Postives = 25/40 (62.50%), Query Frame = -3 
Query:   45 CPNVK*LHCHKARHFS----TNAEKWRDVLENDQKYARAK 152
            C NVK  HCHKA HF        EK R+V ENDQ+YAR K
Sbjct:   58 CSNVKCHHCHKAGHFKHQCFQRTEKRREVRENDQEYARVK 97

HSP 2 Score: 37.7354 bits (86), Expect = 1.473e-9
Identity = 18/37 (48.65%), Postives = 26/37 (70.27%), Query Frame = -1 
Query:  155 RKTKEYPKKQYYFIKQIMQSNNLPKFKCCTCFEECYQ 265
            R+ +EYPKKQ+ F KQ++Q  + PKFK    FEE ++
Sbjct:   18 RQNREYPKKQHNFNKQVVQRISQPKFKFWAYFEEGHR 54
The following BLAST results are available for this feature:
BLAST of SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 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 SMED30029158 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000033246.11.351e-1260.00SMESG000033246.1[more]
SMESG000027262.11.473e-957.50SMESG000027262.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029158 ID=SMED30029158|Name=SMED30029158|organism=Schmidtea mediterranea sexual|type=transcript|length=442bp
AAGTATACAACATCTTGTCATTATAACAATATCGATTTTGGAGCCTTTGC
TCGTGCGTATTTTTGGTCATTTTCTAAAACATCTCTCCATTTTTCAGCAT
TGGTGCTGAAATGTCTTGCTTTATGACAATGGAGTTATTTCACATTCGGA
CAAATTGGTAACACTCTTCAAAACATGTGCAGCATTTAAATTTTGGTAAG
TTATTACTCTGCATAATTTGCTTGATGAAATAGTATTGTTTCTTTGGATA
TTCTTTGGTTTTTCTCAAATTTTGACTGCATTCTCGTTCAGAATATATTT
ATAGCAATGTCCAAGAATATCTGAGGCTTTCCGAGTTATATCTGCGTATT
TTCTATAGGTTTCCATAACTGCTATCAACCTAATTTGCCTACTAAGTTCT
TTATTTATCTTCTCTTGTTTTTTAATTATCTTTTTTATTTTC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell