SMED30012764

Overview
NameSMED30012764
Smed IDSMED30012764
Length (bp)912
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 SMED30012764 (SMED30012764) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012764 (SMED30012764) 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 SMED30012764 (SMED30012764) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012764 (SMED30012764) 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



SMED30012764

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30012764h1SMcG0013645 SmedASXL_013434SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30012764h1SMcG0013645 dd_Smed_v4_5415_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30012764h1SMcG0013645 dd_Smed_v4_5415_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30012764h1SMcG0013645 dd_Smed_v6_340_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30012764 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007224:134..1225 +4346
Homology
[Close]
BLAST of SMED30012764 vs. Planmine SMEST
Match: SMESG000059203.1 (SMESG000059203.1)

HSP 1 Score: 388.652 bits (997), Expect = 4.096e-123
Identity = 237/241 (98.34%), Postives = 238/241 (98.76%), Query Frame = -2 
Query:   78 TPDFXXXXXXXXXXXXXXXXQLASTLSTPAAGRREFFLTFHIINMEFTRDYTDLNSEXXXXXXXXXXXXXXXLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVXXXXXXXXXXXXXXXXXXXIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 800
            TPDFFTNSSQINQTQTISSFQLAST STPAAGRREFFLTF IIN EFTRDYTDLNSELSLLLIR+ISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA
Sbjct: 2403 TPDFFTNSSQINQTQTISSFQLASTFSTPAAGRREFFLTFRIINKEFTRDYTDLNSELSLLLIREISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 2643
[Close]
BLAST of SMED30012764 vs. Planmine SMEST
Match: SMESG000059203.1 (SMESG000059203.1)

HSP 1 Score: 388.652 bits (997), Expect = 4.138e-123
Identity = 237/241 (98.34%), Postives = 238/241 (98.76%), Query Frame = -2 
Query:   78 TPDFXXXXXXXXXXXXXXXXQLASTLSTPAAGRREFFLTFHIINMEFTRDYTDLNSEXXXXXXXXXXXXXXXLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVXXXXXXXXXXXXXXXXXXXIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 800
            TPDFFTNSSQINQTQTISSFQLAST STPAAGRREFFLTF IIN EFTRDYTDLNSELSLLLIR+ISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA
Sbjct: 2418 TPDFFTNSSQINQTQTISSFQLASTFSTPAAGRREFFLTFRIINKEFTRDYTDLNSELSLLLIREISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 2658
[Close]
BLAST of SMED30012764 vs. Planmine SMEST
Match: SMESG000059203.1 (SMESG000059203.1)

HSP 1 Score: 388.652 bits (997), Expect = 4.179e-123
Identity = 237/241 (98.34%), Postives = 238/241 (98.76%), Query Frame = -2 
Query:   78 TPDFXXXXXXXXXXXXXXXXQLASTLSTPAAGRREFFLTFHIINMEFTRDYTDLNSEXXXXXXXXXXXXXXXLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVXXXXXXXXXXXXXXXXXXXIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 800
            TPDFFTNSSQINQTQTISSFQLAST STPAAGRREFFLTF IIN EFTRDYTDLNSELSLLLIR+ISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA
Sbjct: 2422 TPDFFTNSSQINQTQTISSFQLASTFSTPAAGRREFFLTFRIINKEFTRDYTDLNSELSLLLIREISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 2662
[Close]
BLAST of SMED30012764 vs. Planmine SMEST
Match: SMESG000059203.1 (SMESG000059203.1)

HSP 1 Score: 388.267 bits (996), Expect = 4.345e-123
Identity = 237/241 (98.34%), Postives = 238/241 (98.76%), Query Frame = -2 
Query:   78 TPDFXXXXXXXXXXXXXXXXQLASTLSTPAAGRREFFLTFHIINMEFTRDYTDLNSEXXXXXXXXXXXXXXXLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVXXXXXXXXXXXXXXXXXXXIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 800
            TPDFFTNSSQINQTQTISSFQLAST STPAAGRREFFLTF IIN EFTRDYTDLNSELSLLLIR+ISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA
Sbjct: 2429 TPDFFTNSSQINQTQTISSFQLASTFSTPAAGRREFFLTFRIINKEFTRDYTDLNSELSLLLIREISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 2669
[Close]
BLAST of SMED30012764 vs. Planmine SMEST
Match: SMESG000059203.1 (SMESG000059203.1)

HSP 1 Score: 388.267 bits (996), Expect = 4.473e-123
Identity = 237/241 (98.34%), Postives = 238/241 (98.76%), Query Frame = -2 
Query:   78 TPDFXXXXXXXXXXXXXXXXQLASTLSTPAAGRREFFLTFHIINMEFTRDYTDLNSEXXXXXXXXXXXXXXXLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVXXXXXXXXXXXXXXXXXXXIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 800
            TPDFFTNSSQINQTQTISSFQLAST STPAAGRREFFLTF IIN EFTRDYTDLNSELSLLLIR+ISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA
Sbjct: 2433 TPDFFTNSSQINQTQTISSFQLASTFSTPAAGRREFFLTFRIINKEFTRDYTDLNSELSLLLIREISRILSFLPNFGYQLLSFSILQFTSGSIKANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKLVSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGPSLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA 2673
The following BLAST results are available for this feature:
BLAST of SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 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 SMED30012764 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000059203.14.096e-12398.34SMESG000059203.1[more]
SMESG000059203.14.138e-12398.34SMESG000059203.1[more]
SMESG000059203.14.179e-12398.34SMESG000059203.1[more]
SMESG000059203.14.345e-12398.34SMESG000059203.1[more]
SMESG000059203.14.473e-12398.34SMESG000059203.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012764 ID=SMED30012764|Name=SMED30012764|organism=Schmidtea mediterranea sexual|type=transcript|length=912bp
TTTCGATGTATTTATAAAAAATCTGAAAAAACAATAAAATTAATATTAAT
AAACAATTATTCTGAATATTTTTCTCAAGCATCAAATTCTAATCTGAAAT
TATTGTCCGAGGATCTTGGAAGGCTGTCATCGAATTCTAGCCTATAGCAT
GGCTCTCTCAGGATCTCTTCGCTCGTTAATTTTCGAAGCATTGACATGCG
ACGTTCAAAGCTAAGTGATGGGCCTTCTTCAACATCTTGAAACACAAGCT
TGCGATTTCCAAATTTATATCGACGAAGTTGACAAAACATGACGATGAGA
GCAACTAAAACAATAAAAACACAGACACCAATAACGTAGTAGGCCCAGGT
TGAGACGCTGGAGCTAACAAGCTTGTCATTTTGGATATAGGTTGGAATTA
TGGATGAAATTGACAAAGAACTGTTGGAAAGAGAAATAGATTGATTGAAA
GAACTAACAACATTATCATATTGAAGGATGTCATTTGAATTTCCTTTGAG
TTCCATTTTTAAATTTGCTTTAATTGAACCAGACGTAAACTGAAGAATAC
TGAAAGAGAGCAATTGATAACCAAAATTGGGTAAAAAAGAAAGAATTCTG
GATATTTTGCGAATCAAGAGGAGAGAAAGCTCGGAATTCAAATCAGTATA
ATCACGAGTAAATTCCATATTTATAATGTGGAAGGTTAGAAAAAACTCCC
TACGACCAGCAGCAGGAGTAGACAAGGTAGAGGCAAGTTGAAACGAGGAA
ATCGTCTGAGTTTGATTAATTTGAGATGAATTTGTGAAAAAATCAGGAGT
AACAGAAGAAAAAACTCTCGAGGAAGAGGAAAGAACGAGAATTAATTGAA
CCAGAAATACTAGAAATGATAACAGATTTGGTTTCGTTTACAATTGTAGG
AGAGGTTTGTGA
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protein sequence of SMED30012764-orf-1

>SMED30012764-orf-1 ID=SMED30012764-orf-1|Name=SMED30012764-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=198bp
MEFTRDYTDLNSELSLLLIRKISRILSFLPNFGYQLLSFSILQFTSGSIK
ANLKMELKGNSNDILQYDNVVSSFNQSISLSNSSLSISSIIPTYIQNDKL
VSSSVSTWAYYVIGVCVFIVLVALIVMFCQLRRYKFGNRKLVFQDVEEGP
SLSFERRMSMLRKLTSEEILREPCYRLEFDDSLPRSSDNNFRLEFDA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR000082SEA_dom