SMED30021847

Overview
NameSMED30021847
Smed IDSMED30021847
Length (bp)1479
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 SMED30021847 (SMED30021847) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021847 (SMED30021847) 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 SMED30021847 (SMED30021847) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021847 (SMED30021847) 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



SMED30021847

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
head regionSMED30021847SMESG000017151.1 SmedASXL_067966SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30021847SMESG000017151.1 dd_Smed_v4_16489_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30021847SMESG000017151.1 dd_Smed_v4_16489_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30021847SMESG000017151.1 dd_Smed_v4_16489_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30021847SMESG000017151.1 dd_Smed_v6_16489_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021847 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000985:106628..109297 -6764
Homology
[Close]
BLAST of SMED30021847 vs. Planmine SMEST
Match: SMESG000017151.1 (SMESG000017151.1)

HSP 1 Score: 383.259 bits (983), Expect = 7.263e-133
Identity = 200/204 (98.04%), Postives = 202/204 (99.02%), Query Frame = 3 
Query:  252 MASLTISSCDNLFCRNCTLKSNWILVTIDGEYFLQRNTTLCFTEQKKNIQDMFPESYLDGRTPYALSDLECSLKNCFKWSYKYALKILTISSASISCDSVYCQKCTNKGKWSLNTYSSGILLERQVSICMALRRIRITDFFTNNTKSVXXXXXXXXXXXXDMSRGRPEFIWNFGRIIAVILSCCSFISTVLILFVFFCPRKVTY 863
            MASLTISSCDNLFCRNCTLKSNWILVTIDGEYFLQRNTTLCFTEQKKN+QDMFPESYLDGRTPYALSDLECSLKNCFKWSYKYA KILTISSASISCDSVYCQKCTNKGKWSLNTYSSGILLERQVSIC+ALRRIRITDFFTNNTKSVQIIN SIITTSTDMSRGRPEFIWNFGRIIAVILSCCSFISTVLILFVFFCPRKVTY
Sbjct:    1 MASLTISSCDNLFCRNCTLKSNWILVTIDGEYFLQRNTTLCFTEQKKNVQDMFPESYLDGRTPYALSDLECSLKNCFKWSYKYASKILTISSASISCDSVYCQKCTNKGKWSLNTYSSGILLERQVSICVALRRIRITDFFTNNTKSVQIINPSIITTSTDMSRGRPEFIWNFGRIIAVILSCCSFISTVLILFVFFCPRKVTY 204
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BLAST of SMED30021847 vs. Planmine SMEST
Match: SMESG000017181.1 (SMESG000017181.1)

HSP 1 Score: 129.798 bits (325), Expect = 1.549e-34
Identity = 86/251 (34.26%), Postives = 125/251 (49.80%), Query Frame = 3 
Query:  108 MLIKFIFLLYFTLSGRCILIDERNDITCSNKLCSRVRYLLYNVGQTYQ--MASLTISSCDNLFCRNCTLKSNWILVTIDGEYFLQRNTTLCFTEQKKNIQDMFPESYLDGRTPYALSDLECSLKNCFKWSYKYALKILTISSASISCDSVYCQKCTNKGKWSLNTYSSGILLERQVSICMALRRIRITDFFTNNTKSVXXXXXXXXXXXXDMSRGRPEFIWNFGRIIAVILSCCSFISTVLILFVFFCPRK 854
            M    IFLL    +  C  I+ERNDITC+N+ C+ VRY LY   Q+Y   +     S C ++ C NC+ K NW+L    G YFL R+T  C T+  +N  ++FP S     +P  ++D+ CS   C K++Y +    L       +C    C+ C     W     +S  LL+R VS C ++ RI + DFF                   D      EF W+ GRI++VI+SC SF++ ++IL V FC + 
Sbjct:    1 MAFLVIFLLLLRNALGCSFINERNDITCANRTCNNVRYRLYYDDQSYHYYVNVAGESVCPSVNCNNCSYKGNWMLGKASGTYFLYRSTNSCSTDSIRNFTEIFPSS-----SPLNVTDIACSNYGCSKYNYLFESSKLYTKYLG-NCSYPSCEGCKTLTPWQYVNGNSYNLLQRNVSSCPSITRINMEDFF----------------RRLDQISFVKEF-WDGGRILSVIISCVSFVALIIILSVCFCKKP 228
[Close]
BLAST of SMED30021847 vs. Planmine SMEST
Match: SMESG000017240.1 (SMESG000017240.1)

HSP 1 Score: 124.405 bits (311), Expect = 1.093e-32
Identity = 63/183 (34.43%), Postives = 102/183 (55.74%), Query Frame = 3 
Query:  126 FLLYFTLSGRCILIDERNDITCSNKLCSRVRYLLYNVGQTYQMASLTISSCDNLFCRNCTLKSNWILVTIDGEYFLQRNTTLCFTEQKKNIQDMFPESYLDGRTPYALSDLECSLKNCFKWSYKYALKILTISSASISCDSVYCQKCTNKGKWSLNTYSSGILLERQVSICMALRRIRITDFF 674
            FLL+  LS  C +I+ERND++C+   CS +RY +      Y+++S  ISSCD   C+NC  KS+W L+ I G  ++ RNT  C +E  K  +++FP  Y        + D+ C+  +C+K  Y+     + I+     C   YC+KC    KW+   ++   +L R+ ++C A  +I+ITD+F
Sbjct:    5 FLLFIHLSAGCKIINERNDVSCNKGKCSIIRYQISGAKSNYELSSRLISSCDPTKCKNCAHKSDWSLLKIQGVSYVVRNTNSCLSENAKEPKEIFPRKY------SKVLDIRCNSYSCWKDIYQVRTNYMKITPQG-PCSDDYCKKCYFSDKWNFTKFAGSPILTRKTTLCEASSKIKITDYF 180
[Close]
BLAST of SMED30021847 vs. Planmine SMEST
Match: SMESG000017240.1 (SMESG000017240.1)

HSP 1 Score: 124.79 bits (312), Expect = 1.257e-32
Identity = 66/196 (33.67%), Postives = 108/196 (55.10%), Query Frame = 3 
Query:   90 FPFVKVMLIKFI-FLLYFTLSGRCILIDERNDITCSNKLCSRVRYLLYNVGQTYQMASLTISSCDNLFCRNCTLKSNWILVTIDGEYFLQRNTTLCFTEQKKNIQDMFPESYLDGRTPYALSDLECSLKNCFKWSYKYALKILTISSASISCDSVYCQKCTNKGKWSLNTYSSGILLERQVSICMALRRIRITDFF 674
             P V++ +   I FLL+  LS  C +I+ERND++C+   CS +RY +      Y+++S  ISSCD   C+NC  KS+W L+ I G  ++ RNT  C +E  K  +++FP  Y        + D+ C+  +C+K  Y+     + I+     C   YC+KC    KW+   ++   +L R+ ++C A  +I+ITD+F
Sbjct:    1 MPNVQLYISMIIHFLLFIHLSAGCKIINERNDVSCNKGKCSIIRYQISGAKSNYELSSRLISSCDPTKCKNCAHKSDWSLLKIQGVSYVVRNTNSCLSENAKEPKEIFPRKY------SKVLDIRCNSYSCWKDIYQVRTNYMKITPQG-PCSDDYCKKCYFSDKWNFTKFAGSPILTRKTTLCEASSKIKITDYF 189
[Close]
BLAST of SMED30021847 vs. Planmine SMEST
Match: SMESG000017162.1 (SMESG000017162.1)

HSP 1 Score: 114.39 bits (285), Expect = 4.642e-29
Identity = 81/248 (32.66%), Postives = 116/248 (46.77%), Query Frame = 3 
Query:  108 MLIKFIFLLYFTLSGRCILIDERNDITCSNKLCSRVRYLLYNVGQTYQMASLTISSCDNLFCRNCTLKSNWILVTIDGEYFLQRNTTLCFTEQKKNIQDMFPESYLDGRTPYALSDLECSLKNCFKWSYKYALKILTISSASISCDSVYCQKCTNKGKWSLNTYSSGILLERQVSICMALRRIRITDFFTNNTKSVXXXXXXXXXXXXDMSRGRPEFIWNFGRIIAVILSCCSFISTVLILFVFFCPR 851
            M+  F+ L  F      I IDERNDI+C+   CS   Y LY  G    + S   SSCD+  C  CT+KSNW L+  +G Y++ R T+ C  E+ K I  MFP          + SD+ C    C K+ YK +     I+S    C++  C+KC +   W + +     L+ R  S C A   I + DFF     S +                     WN   I+AVI+SC SF++ V++L + FC +
Sbjct:    1 MIFYFLILDVFYFCQAKIFIDERNDISCNFGNCSVYAYQLYQNGNGSLLVSSFKSSCDSKSCDGCTIKSNWALIWKNGRYYMTRITSNCQAEKSKFINYMFPS------PKSSFSDISCDFGKCVKYKYKIS-NTRFITSLIGPCENSNCKKCNDLSYWEIESVIIPSLV-RSSSRCSAFDEILMEDFFIVPASSTESS------------------FWNTSVIVAVIISCLSFVTLVIVLSICFCTK 222
The following BLAST results are available for this feature:
BLAST of SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 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 SMED30021847 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000017151.17.263e-13398.04SMESG000017151.1[more]
SMESG000017181.11.549e-3434.26SMESG000017181.1[more]
SMESG000017240.11.093e-3234.43SMESG000017240.1[more]
SMESG000017240.11.257e-3233.67SMESG000017240.1[more]
SMESG000017162.14.642e-2932.66SMESG000017162.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021847 ID=SMED30021847|Name=SMED30021847|organism=Schmidtea mediterranea sexual|type=transcript|length=1479bp
TCTTCCGATCTGCAGTTAGGAAAAATCAATAAAATATTTCATTTTTATTT
TCTTGCTTTTTGATTGGTTGATTTAAATCTTTGATATAATTTCCTTTTGT
AAAAGTTATGTTAATTAAATTCATATTTTTATTGTATTTTACACTCAGCG
GAAGATGTATACTAATTGATGAACGGAATGACATAACATGCAGTAATAAA
CTTTGCAGTAGGGTCCGTTACCTTCTGTACAATGTGGGCCAAACTTATCA
AATGGCTTCGTTGACCATTTCTAGCTGTGATAATTTATTCTGCAGGAATT
GCACCTTGAAATCAAATTGGATCTTAGTGACCATCGATGGAGAGTACTTC
TTACAAAGGAATACAACATTGTGTTTTACAGAACAAAAGAAAAACATTCA
AGATATGTTTCCAGAAAGTTATCTCGATGGACGAACGCCCTATGCGCTAT
CTGATTTGGAATGTTCTTTAAAGAATTGCTTCAAATGGTCATACAAATAT
GCATTAAAAATTCTCACAATATCGTCAGCTTCAATATCGTGTGACTCGGT
TTACTGTCAAAAATGTACAAACAAAGGAAAATGGTCTTTGAATACATATT
CTTCAGGAATTCTTTTAGAACGGCAAGTTTCAATCTGTATGGCATTAAGA
AGAATAAGAATAACAGATTTTTTTACAAATAATACAAAATCAGTTCAGAT
AATAAATCAATCAATTATAACAACTTCCACTGACATGTCAAGGGGGAGGC
CAGAATTTATTTGGAATTTCGGACGAATAATAGCTGTTATTTTAAGTTGT
TGTTCTTTCATATCGACTGTCTTAATTTTGTTTGTTTTCTTTTGCCCTCG
CAAAGTTACTTACTGTTAATGGACAATTTTTTTTCTATTTTACATTCGCA
CATTTTCAATTTTCTTTTTTAATCTACACTTTCAAATCGGATTTTGCAAT
AATTTTGTCATAATTAATTAGAGTTATTTCAGTGTTAGTTTCCACATTTA
TTATGGCATAATATATAATCTTGTCTATTTCTCATGGTTATTTGGTAACA
AAATTGTAAAATTATCTTAATTTTAGAAAATTTTTAATTTTTTGTTTTCG
TCCCTCCCTCGACTTTAAAAACTAAAACCAAACGAAAAATAATTAATAAT
TAACTAGGTAAATTATTTTCTTTTTATAAGTTAAACCTATAGAGACCCTG
TAAATATTGAAGAAATAATTATTGAAGTTGTAAGACCAATTGCTAATAAA
CCACCACAGAAAATCCTGCGCTTGATATGGATAAAATTCCTGCAATTGAA
ACGCATGTAATTGTTATAGTGCAATCAGCCTTAGTCCGTCTGGTTTCAAT
TTTTTTATAATGAATTAATCTTTCATCAAGTTTCTTTTCTCCAATAGGAA
TTCATTTACTTTATTAGGTTCCAGAATATTTTGAAGCATAATCATTGATG
GGGTGTAAAACTTATCTCAAACAAGAGAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head