SMED30009555

Overview
NameSMED30009555
Smed IDSMED30009555
Length (bp)2389
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30009555 (SMED30009555) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009555 (SMED30009555) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30009555

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30009555 SmedASXL_000154SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30009555 SmedASXL_002030SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30009555 dd_Smed_v4_79387_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009555 dd_Smed_v4_79387_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30009555 dd_Smed_v4_79387_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30009555 dd_Smed_v4_57399_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009555 dd_Smed_v4_57399_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30009555 dd_Smed_v4_57399_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30009555 dd_Smed_v6_57399_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
The following BLAST results are available for this feature:
BLAST of SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 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 SMED30009555 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009555 ID=SMED30009555|Name=SMED30009555|organism=Schmidtea mediterranea sexual|type=transcript|length=2389bp
TTTCAATTTCTTAAAATACTTTCAATAATTTTTAATTTTGGATAAAATTT
GTGTTGCAAGTGGAATTTCATTAAATTTATAATGGGGATTATTGACATTG
AAAAATTCTCGGCATATTTCAAATTACTTCACAATGAAGTATACAAATTC
ACTGGAAAGGCTCAAGCTGATATTTTGAATATTCTAATTTATATTTGGAT
TTTATTATCAGCTGTTGTGGTCTGCTCGGTTTACTTCTGGACAAACAATG
AGCTATTAAGATTGCTCGCGAGAATGAGGTTGTCGAAACAATACCAGATT
TGCTGGAGCTGGCTACAGTCGGACCAACTCGGCAGAAAAGAGTCAAAATC
AAATCGACTACTGTGAAAATGCATCGAATGAATAAATCTGTTGAGTATCA
TGCAAAGGAAACTGTCAACCCCGATAAATTAATCCAGGCCCCCAGTCAGC
CGGCAGCAGTGATTGCCACAGAGGCTAAAGGCTGGGCAAATGCTGTTATC
AGATTTTTATTCAACAGCTCACGCTGCAAACAACGGATATCAGCAAAAAT
GATGGAAATACTAAACGAAATCCTGGACAACTCAACATGCCATTCCATGA
AGGTGTCCGTTATCTCAGTGTCATTCGGATCGAGGCTCCCGCAAATTACA
GATAATGTTAGTGAAGCTGAGGAAAATTTGTCATTTTTTTCTTGTTGTGT
GAGCCTACTAATCCCGCAGTTGGTGATTGCAGTGTCGTTCAGTGACACTA
TCAAAGAAGACTGTAGTTTTGAAAAATGCATGATAAACATCTCTGAATTG
CTGTTGAAAATAAATATTGAGAATTATTTTACAGAGGAAGCCCTGAAGAT
GAAGATCAGTTTCCACGACAAAGTCATCGCTCATTCTCATATTGAGGCAC
CGAATATGGATGCAATTGCATTGCAATTAGTGAAGCATGAAGTTTGTTCT
GCATTTGACAAGGGCGTGTTTGAGTTGGAATTCCGAATTGACGATGGGAC
TGATTTGTTGAGTGAGGAAGTTCATATCTCTCATCACCATGCCAAGGACA
AATCTACTTCACCCCGAACCATTTTACATTTCGATACCAGTTTGCTCGTG
GACATCGATCCGTCGAAGCTCGACACAATGGAGCAAGATAAATTCGTGAC
CAGATGGATTTCCGGAAAGATCGAGTCTAATTTTATTTCCTAAATAGTAA
AAGCTGTCTAGTCCCATCTCCCAAGGCTGTTCTGTATTGCGTTTGGGATA
GCTGAACTACTTTCCCTTATCATGTGGCATAAATTATATGAAAATCATAG
ACATCGTCCATGGAAAAGAATGGAAGCCGACAAGAAAAACTGCTGACAAT
ACATTACGTTATGATCCCTTTCCTTATCAGTGAAAGACTTGATGAAATCT
TTCTTGTCATTCATATTGATAATCCCAAGCAATACTACAAGTCCCTAGTG
AGCTCCTTCAGGAAAACCGAGACTGGAATTGAAAATATATTTGCCTGTGT
CAATGCCACATTTTTTATTGGCCAACCTTCAGCTGTTCTGAAATTTATTT
TACAAACTGAAAATTCTCTAATATTGAGATCAGGACAAATTCATGTCACT
GAACACCTTCAGGACTCCATTTCGTTTTTGAGCATGAACCTTCATCTTCC
CATTGAGAGAGAGAATGATTTTATCTTTTCAACTAATATGGAATTTGCAA
CCCTCTCTCTGTTTGTACAAAGCAAACAGATGTGACACTCTCCTTTCAGA
CGAGCACACACTAGAATTCCTCAGAACGGGCTATCGAAAATTGGACAATA
TCGAGGATGAAATGATTGGTCAAATGGCAGAATATTCCACCGGAGAAGAT
TTTGGAGATAATTTCGTGAATTTTATAAATTCCCAAGGACTGGTTGTTGA
TCACAAAGAAATAGAGGTGATGATAAACCGGGAAAATCATATTCGATGTG
GAAAACATTCTGACCACAACAGAAAGGTCGAGTGGTATAAGCGACTGCCA
ACTAAAGCATTTCAAAAATGTAAGACAAAATTGTATGGGAAAATTCAAAT
GGAAAAACGAACCTTGTTCTCGGTTTGGAATCATCGATCACAGCCAAGAA
AGGACTGGAATAGTAAAGAAATTATTTGGTTATTCTTAGCAATCTATTTA
GTATCCCGTGATTCAGAGCAATGTGTGTCGATGGATTCTATTCCGACAAC
TGAGAAACTCAGGAAATCTCACCTGTACAACTCAGCCCCGAATGTTGTCA
AGAGTCCTCAGCATCTCAAACAAAAAGTGAAGCGAAAATAAGTTTGACAA
TAGATCCTTTCATTGTGATATTGAGGACTTGCGGACAGCTGGCAGTTACC
ATTGTTGTCATTTATTCGTTGTTTTATTCAATTAGCTAG
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protein sequence of SMED30009555-orf-1

>SMED30009555-orf-1 ID=SMED30009555-orf-1|Name=SMED30009555-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=142bp
MEKNGSRQEKLLTIHYVMIPFLISERLDEIFLVIHIDNPKQYYKSLVSSF
RKTETGIENIFACVNATFFIGQPSAVLKFILQTENSLILRSGQIHVTEHL
QDSISFLSMNLHLPIERENDFIFSTNMEFATLSLFVQSKQM*
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protein sequence of SMED30009555-orf-2

>SMED30009555-orf-2 ID=SMED30009555-orf-2|Name=SMED30009555-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=209bp
MILSFQLIWNLQPSLCLYKANRCDTLLSDEHTLEFLRTGYRKLDNIEDEM
IGQMAEYSTGEDFGDNFVNFINSQGLVVDHKEIEVMINRENHIRCGKHSD
HNRKVEWYKRLPTKAFQKCKTKLYGKIQMEKRTLFSVWNHRSQPRKDWNS
KEIIWLFLAIYLVSRDSEQCVSMDSIPTTEKLRKSHLYNSAPNVVKSPQH
LKQKVKRK*
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protein sequence of SMED30009555-orf-3

>SMED30009555-orf-3 ID=SMED30009555-orf-3|Name=SMED30009555-orf-3|organism=Schmidtea mediterranea sexual|type=polypeptide|length=275bp
MHRMNKSVEYHAKETVNPDKLIQAPSQPAAVIATEAKGWANAVIRFLFNS
SRCKQRISAKMMEILNEILDNSTCHSMKVSVISVSFGSRLPQITDNVSEA
EENLSFFSCCVSLLIPQLVIAVSFSDTIKEDCSFEKCMINISELLLKINI
ENYFTEEALKMKISFHDKVIAHSHIEAPNMDAIALQLVKHEVCSAFDKGV
FELEFRIDDGTDLLSEEVHISHHHAKDKSTSPRTILHFDTSLLVDIDPSK
LDTMEQDKFVTRWISGKIESNFIS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head