SMED30002790

Overview
NameSMED30002790
Smed IDSMED30002790
Length (bp)675
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



SMED30002790

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30002790 SmedASXL_077818SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30002790 SmedASXL_077818SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30002790 dd_Smed_v4_49_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002790 dd_Smed_v4_49_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30002790 dd_Smed_v4_49_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
SMED30002790 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.030767:2938..3602 -3271
v31.014947:835..1500 -3169
v31.014947:7750..8446 +2997
Homology
[Close]
BLAST of SMED30002790 vs. Planmine SMEST
Match: SMESG000044563.1 (SMESG000044563.1)

HSP 1 Score: 171.4 bits (433), Expect = 3.204e-55
Identity = 84/84 (100.00%), Postives = 84/84 (100.00%), Query Frame = -1 
Query:  298 MNGQLSKIFIDQFGRHSNSTRNKNIKIFIDLIKRISVFLSRILCNLPFQLCKYSSKELLHDILQCISHRSFDKPCTSPAHHQLA 549
            MNGQLSKIFIDQFGRHSNSTRNKNIKIFIDLIKRISVFLSRILCNLPFQLCKYSSKELLHDILQCISHRSFDKPCTSPAHHQLA
Sbjct:    1 MNGQLSKIFIDQFGRHSNSTRNKNIKIFIDLIKRISVFLSRILCNLPFQLCKYSSKELLHDILQCISHRSFDKPCTSPAHHQLA 84
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BLAST of SMED30002790 vs. Planmine SMEST
Match: SMESG000044560.1 (SMESG000044560.1)

HSP 1 Score: 131.339 bits (329), Expect = 9.401e-40
Identity = 63/63 (100.00%), Postives = 63/63 (100.00%), Query Frame = 3 
Query:  264 AVFIMFFLVALTQADDEQEKYKACQKTYVKCIAGCRGAVPCSNTCTIEMEDCTGYEKGTPKSV 452
            AVFIMFFLVALTQADDEQEKYKACQKTYVKCIAGCRGAVPCSNTCTIEMEDCTGYEKGTPKSV
Sbjct:    4 AVFIMFFLVALTQADDEQEKYKACQKTYVKCIAGCRGAVPCSNTCTIEMEDCTGYEKGTPKSV 66
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BLAST of SMED30002790 vs. Planmine SMEST
Match: SMESG000044561.1 (SMESG000044561.1)

HSP 1 Score: 129.798 bits (325), Expect = 3.987e-39
Identity = 62/63 (98.41%), Postives = 62/63 (98.41%), Query Frame = 3 
Query:  264 AVFIMFFLVALTQADDEQEKYKACQKTYVKCIAGCRGAVPCSNTCTIEMEDCTGYEKGTPKSV 452
            AVFIMFFLVALTQADDEQEKYKACQKTYVKCI GCRGAVPCSNTCTIEMEDCTGYEKGTPKSV
Sbjct:    4 AVFIMFFLVALTQADDEQEKYKACQKTYVKCIGGCRGAVPCSNTCTIEMEDCTGYEKGTPKSV 66
The following BLAST results are available for this feature:
BLAST of SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 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 SMED30002790 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000044563.13.204e-55100.00SMESG000044563.1[more]
SMESG000044560.19.401e-40100.00SMESG000044560.1[more]
SMESG000044561.13.987e-3998.41SMESG000044561.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002790 ID=SMED30002790|Name=SMED30002790|organism=Schmidtea mediterranea sexual|type=transcript|length=675bp
TCGCATTTTTTTTTTTTTTTTTTATATTCAAAATTGTATTTACACAGATT
TTAAGAGATTTCTAAAATGTTTTGATAGAGCAATTAACAAAATAAATAAT
CTCCAGTCAATATAAACAAAATTCTCAATTACAGAAATATATAAAACCAA
TTGATAATACAATAAAAACATTCACAAATAACTCAATATGATCAAAGTAA
AATTGAATTCATTTGATTATAATTTAATAATTTGATAATTTAATAATTTT
TGGCTATTTCTAGGCAGTTTTCATCATGTTCTTTCTGGTGGCTCTCACGC
AAGCTGATGATGAGCAGGAGAAGTACAAGGCTTGTCAAAAGACCTATGTG
AAATGCATTGCAGGATGTCGTGGAGCAGTTCCTTGCTCGAATACTTGCAC
AATTGAAATGGAAGATTGCACAGGATACGAGAAAGGAACACCGAAATCCG
TTTGATTAAGTCAATAAATATTTTAATATTTTTATTCCGTGTTGAATTTG
AATGTCTTCCAAACTGGTCAATAAAGATCTTTGATAATTGTCCATTCATT
GGAGAGCTTGAGATTTATTAATTAAATAAAGCGAATGAAGATTAGATTAA
ACCTTTCACGGAATGGTAACACCATTCAAGTCCGGGAGGAAAACTTTGTT
ATATTTAGGCTTCAATAAAATATTG
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