SMED30011909

Overview
NameSMED30011909
Smed IDSMED30011909
Length (bp)363
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ 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




 

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 SMED30011909 (SMED30011909) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011909 (SMED30011909) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30011909 (SMED30011909) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011909 (SMED30011909) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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




SMED30011909

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30011909SMESG000027686.1 Contig2364GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30011909SMESG000027686.1 Contig2364GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30011909SMESG000027686.1 Contig2364GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30011909SMESG000012131.1 SMESG000012127.1 Contig2364GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30011909SMESG000012131.1 SMESG000012127.1 Contig2364GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30011909SMESG000012131.1 SMESG000012127.1 Contig2364GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
headSMED30011909SMESG000012131.1 SmedASXL_032732SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011909 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000238:178825..179384 -1718
Homology
BLAST of SMED30011909 vs. Planmine SMEST
Match: SMESG000012131.1 (SMESG000012131.1)

HSP 1 Score: 211.846 bits (538), Expect = 3.105e-70
Identity = 101/103 (98.06%), Postives = 102/103 (99.03%), Query Frame = 2
Query:    2 MSIRASDIYSAPEINDYGEANFNSDVWSLGRTVCYMFFRDINKMNNYLVSLDSQKIFGRIFGHSACNYGIYLGLHDLLGRMLEKDHNRRFGAGDVLSHYFITG 310
            MSIRASDIYSAPEIN+YG ANFNSDVWSLGRTVCYMFFRDINKMNNYLVSLDSQKIFGRIFGHSACNYGIYLGLHDLLGRMLEKDHNRRFGAGDVLSHYFITG
Sbjct:  161 MSIRASDIYSAPEINNYGVANFNSDVWSLGRTVCYMFFRDINKMNNYLVSLDSQKIFGRIFGHSACNYGIYLGLHDLLGRMLEKDHNRRFGAGDVLSHYFITG 263          
BLAST of SMED30011909 vs. Planmine SMEST
Match: SMESG000012127.1 (SMESG000012127.1)

HSP 1 Score: 117.472 bits (293), Expect = 1.012e-33
Identity = 63/103 (61.17%), Postives = 69/103 (66.99%), Query Frame = 2
Query:    2 MSIRASDIYSAPEINDYGEANFNSDVWSLGRTVCYMFFRDINKMNNYLVSLDSQKIFGRIFGHSACNYGIYLGLHDLLGRMLEKDHNRRFGAGDVLSHYFITG 310
            MSIRASDIYSAPEINDYGEANFNSDVWSLGRTVCYM  RDIN ++NY VS D                     L+DLL  MLE+D + R  A +VLSH FITG
Sbjct:  140 MSIRASDIYSAPEINDYGEANFNSDVWSLGRTVCYMITRDINDLDNYFVSSD---------------------LYDLLNGMLEEDPDDRLEADEVLSHCFITG 221          
BLAST of SMED30011909 vs. Planmine SMEST
Match: SMESG000012127.1 (SMESG000012127.1)

HSP 1 Score: 117.087 bits (292), Expect = 2.274e-33
Identity = 63/103 (61.17%), Postives = 69/103 (66.99%), Query Frame = 2
Query:    2 MSIRASDIYSAPEINDYGEANFNSDVWSLGRTVCYMFFRDINKMNNYLVSLDSQKIFGRIFGHSACNYGIYLGLHDLLGRMLEKDHNRRFGAGDVLSHYFITG 310
            MSIRASDIYSAPEINDYGEANFNSDVWSLGRTVCYM  RDIN ++NY VS D                     L+DLL  MLE+D + R  A +VLSH FITG
Sbjct:  161 MSIRASDIYSAPEINDYGEANFNSDVWSLGRTVCYMITRDINDLDNYFVSSD---------------------LYDLLNGMLEEDPDDRLEADEVLSHCFITG 242          
The following BLAST results are available for this feature:
BLAST of SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 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 SMED30011909 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000012131.13.105e-7098.06SMESG000012131.1[more]
SMESG000012127.11.012e-3361.17SMESG000012127.1[more]
SMESG000012127.12.274e-3361.17SMESG000012127.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011909 ID=SMED30011909|Name=SMED30011909|organism=Schmidtea mediterranea sexual|type=transcript|length=363bp
AATGAGTATCCGAGCATCAGATATTTATTCAGCTCCAGAAATAAATGATT
ATGGAGAGGCAAATTTCAATTCCGACGTTTGGAGTTTGGGACGCACTGTT
TGTTATATGTTTTTCCGAGATATAAACAAAATGAATAATTATTTGGTATC
TTTGGATTCACAGAAGATTTTTGGTAGAATTTTTGGACACTCTGCTTGTA
ATTATGGCATATATTTGGGTTTACACGACCTTCTTGGTAGGATGCTTGAG
AAGGATCATAATAGGAGATTTGGAGCAGGTGATGTTCTCAGCCATTACTT
CATAACTGGGCTGAACTCTTTGAATTTCTTTAACTTTTTAATTTAATATT
TGTGTCTTAATAA
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protein sequence of SMED30011909-orf-1

>SMED30011909-orf-1 ID=SMED30011909-orf-1|Name=SMED30011909-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
MSIRASDIYSAPEINDYGEANFNSDVWSLGRTVCYMFFRDINKMNNYLVS
LDSQKIFGRIFGHSACNYGIYLGLHDLLGRMLEKDHNRRFGAGDVLSHYF
ITGLNSLNFFNFLI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR000719Prot_kinase_dom
IPR011009Kinase-like_dom_sf
Vocabulary: molecular function
TermDefinition
GO:0005524ATP binding
GO:0004672protein kinase activity
GO:0000166nucleotide binding
GO:0004674protein serine/threonine kinase activity
GO:0016301kinase activity
Vocabulary: biological process
TermDefinition
GO:0006468protein phosphorylation
GO:0016310phosphorylation