SMED30011447

Overview
NameSMED30011447
Smed IDSMED30011447
Length (bp)905
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 SMED30011447 (SMED30011447) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011447 (SMED30011447) 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 SMED30011447 (SMED30011447) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011447 (SMED30011447) 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



SMED30011447

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30011447h1SMcG0020137 Contig47967newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011447h1SMcG0020137 Contig47967uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011447h1SMcG0020138 Contig47967newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011447h1SMcG0020138 Contig47967uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30011447h1SMcG0020137 dd_Smed_v4_1321_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011447h1SMcG0020137 dd_Smed_v4_1321_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30011447h1SMcG0020137 SMED30011447smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30011447h1SMcG0020137 SMED30011447smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Category 3 cellSMED30011447h1SMcG0020137 dd_Smed_v6_1321_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30011447h1SMcG0020137 dd_Smed_v4_1321_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011447 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000717:46247..47151 -4525
Homology
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BLAST of SMED30011447 vs. TrEMBL
Match: A0A0A1CQX9 (Pmp-10 (Fragment) OS=Schmidtea mediterranea OX=79327 GN=pmp-10 PE=2 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 2.631e-9
Identity = 38/126 (30.16%), Postives = 59/126 (46.83%), Query Frame = -3 
Query:  319 ECQNLLKKVISCDGDWKALDKYCAIKFETHDKVCERRYFYLDTRCNTDYEKYDKVCNYRER--TGKCIKMLDRIDRYCVAKYAILDMNCDSDYRKLDKHCNQGSKELQHRCLAIFSNYHRVCKDEI 690
            +C +L+ +VISCD  ++ +D YC  K    D  C R++  L   CN    K    CN +    T  C +  DR+D+ C      L   C   YRK+D  CN+   ++  +C  I+  Y   C+  +
Sbjct:   25 QCNDLIPEVISCDSAYETIDNYCERKATEIDSFCNRKFSKLTESCNKAENKIKLDCNTKVGYITASCGRRFDRLDKVCRISSTTLSRKCTKKYRKMDNKCNKKYGKINVKCKRIYYRYKDFCETGV 150
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BLAST of SMED30011447 vs. Planmine SMEST
Match: SMESG000034829.1 (SMESG000034829.1)

HSP 1 Score: 348.591 bits (893), Expect = 2.430e-122
Identity = 168/168 (100.00%), Postives = 168/168 (100.00%), Query Frame = -3 
Query:  250 MLLYFVIFVWISISTISGNNEECQNLLKKVISCDGDWKALDKYCAIKFETHDKVCERRYFYLDTRCNTDYEKYDKVCNYRERTGKCIKMLDRIDRYCVAKYAILDMNCDSDYRKLDKHCNQGSKELQHRCLAIFSNYHRVCKDEIELKMLKSFRNAAKNEEKTMKQTS 753
            MLLYFVIFVWISISTISGNNEECQNLLKKVISCDGDWKALDKYCAIKFETHDKVCERRYFYLDTRCNTDYEKYDKVCNYRERTGKCIKMLDRIDRYCVAKYAILDMNCDSDYRKLDKHCNQGSKELQHRCLAIFSNYHRVCKDEIELKMLKSFRNAAKNEEKTMKQTS
Sbjct:    1 MLLYFVIFVWISISTISGNNEECQNLLKKVISCDGDWKALDKYCAIKFETHDKVCERRYFYLDTRCNTDYEKYDKVCNYRERTGKCIKMLDRIDRYCVAKYAILDMNCDSDYRKLDKHCNQGSKELQHRCLAIFSNYHRVCKDEIELKMLKSFRNAAKNEEKTMKQTS 168
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BLAST of SMED30011447 vs. Planmine SMEST
Match: SMESG000076142.1 (SMESG000076142.1)

HSP 1 Score: 73.559 bits (179), Expect = 1.619e-15
Identity = 44/153 (28.76%), Postives = 67/153 (43.79%), Query Frame = -3 
Query:  328 FSIFLALNSIVMLLYFVIFVWISISTISGNNEECQNLLKKVISCDGDWKALDKYCAIKFETHDKVCERRYFYLDTRCNTDYEKYDKVCNYRERTGKCIKMLDRIDRYCVAKYAILDMNCDSDYRKLDKHCNQGSKELQHRCLAIFSNYHRVCK 786
            +S F  L  I++L YF        + +      C  L +    CDG WK +D +C   ++  D  C+ RY  LD  C + Y+     C+    T  C       + YC  +   +D+ CD  Y  LDK C++  K L  +C  I+  Y R C+
Sbjct:    3 YSFFSGL--ILVLFYF--------ANVESRQTACYVLTQTSKKCDGLWKQIDNWCVSAYKKLDTYCDTRYVNLDKDCKSKYKNLAVNCHKERLTEDCSSSYKNTNEYCANELEKIDVKCDPMYTNLDKQCDKSYKNLIDQCNPIYKKYRRFCQ 145
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BLAST of SMED30011447 vs. Planmine SMEST
Match: SMESG000068428.1 (SMESG000068428.1)

HSP 1 Score: 76.2554 bits (186), Expect = 3.308e-15
Identity = 38/123 (30.89%), Postives = 58/123 (47.15%), Query Frame = -3 
Query:  328 ECQNLLKKVISCDGDWKALDKYCAIKFETHDKVCERRYFYLDTRCNTDYEKYDKVCNYRER--TGKCIKMLDRIDRYCVAKYAILDMNCDSDYRKLDKHCNQGSKELQHRCLAIFSNYHRVCK 690
            +C +L+ +VISCD  ++ +D YC  K    D  C R++  L   CN    K    CN +    T  C +  DR+D+ C      L   C   YRK+D  CN+   ++  +C  I+  Y   C+
Sbjct:   43 QCNDLIPEVISCDSAYETIDNYCERKATEIDSFCNRKFSKLTESCNKAENKIKLDCNTKVGYITASCGRRFDRLDKVCRISSTTLSRKCTKKYRKMDNKCNKKYGKINVKCKRIYYRYKDFCE 165
[Close]
BLAST of SMED30011447 vs. Planmine SMEST
Match: SMESG000068743.1 (SMESG000068743.1)

HSP 1 Score: 70.4774 bits (171), Expect = 3.307e-13
Identity = 35/127 (27.56%), Postives = 62/127 (48.82%), Query Frame = -3 
Query:  319 EECQNLLKKVISCDGDWKALDKYCAIKFETHDKVCERRYFYLDTRCNTDYEKYDKVCNYRER--TGKCIKMLDRIDRYCVAKYAILDMNCDSDYRKLDKHCNQGSKELQHRCLAIFSNYHRVCKDEI 693
            E+C  L+ +  SCD  ++ +DKYC  K  + DK C+  +  L  +CNT      + C  +    T +C ++ +R+D  C    +    +C   YRK+D  C +   ++  +C  IF  Y   C+ ++
Sbjct:   42 EQCNLLIPEADSCDQAYQTVDKYCDEKASSIDKECDISFKKLVEKCNTAENSIKERCQKKNGYVTAECGRLFERLDNVCRIVSSTQSRHCTKLYRKMDNECYKKYSKITLKCKRIFDRYKDFCESDM 168
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BLAST of SMED30011447 vs. Planmine SMEST
Match: SMESG000072142.1 (SMESG000072142.1)

HSP 1 Score: 53.5286 bits (127), Expect = 6.666e-9
Identity = 36/134 (26.87%), Postives = 65/134 (48.51%), Query Frame = -3 
Query:  364 IVMLLYFVIFVWISISTISG--NNEECQNLLKKVISCDGDWKALDKYCAIKFETHDKVCERRYFYLDTRCNTDYEKYDKVCNYRERTGKCIKMLDRIDRYCVAKYAILDMNCDSDYRKLDKHCNQGSKELQHRC 759
            ++ + +F+    +++  +S   N+ +C  +L K+          D+ C  K+   D  C+ RY +L   C+ +Y+K    C     + +CI    R+DR C+  Y  +D  CD  Y  LD HC++  K +Q +C
Sbjct:    1 MIQIGFFMTLALLNVECVSKSKNSADCLTMLDKI----------DRECDRKYLVLDNHCDSRYAHLHKTCDINYDKLSGRCK-NNMSMRCILKYGRLDRKCLGAYDRVDTFCDKRYNVLDTHCDELYK-IQEKC 122
The following BLAST results are available for this feature:
BLAST of SMED30011447 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 SMED30011447 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 SMED30011447 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 SMED30011447 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 SMED30011447 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 SMED30011447 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 SMED30011447 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 SMED30011447 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A0A1CQX92.631e-930.16Pmp-10 (Fragment) OS=Schmidtea mediterranea OX=793... [more]
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BLAST of SMED30011447 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 SMED30011447 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 SMED30011447 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 SMED30011447 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 SMED30011447 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 SMED30011447 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000034829.12.430e-122100.00SMESG000034829.1[more]
SMESG000076142.11.619e-1528.76SMESG000076142.1[more]
SMESG000068428.13.308e-1530.89SMESG000068428.1[more]
SMESG000068743.13.307e-1327.56SMESG000068743.1[more]
SMESG000072142.16.666e-926.87SMESG000072142.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011447 ID=SMED30011447|Name=SMED30011447|organism=Schmidtea mediterranea sexual|type=transcript|length=905bp
TTGTAAACCAAAATTTTTATTTTATTAATTATTTTATATAAATTAAAGCA
TCTAGGGCAAATGAAAAATAATGACATTTCCATGAAAATTACATCAAGAT
AAAAATTTAATTTTACAATAAAATTATCAAAAATTTCAGTTTATTTGAAA
ATTTCAATTTTATCCTTGCAAAAAATTTTACATTGTTTTCGTCTGAGTTT
TACTCATTTTTGTTTCAACAACTTTTTTCACTAATTTGACTTCTTTTTTG
CTAGTTTGTTTCATCGTTTTCTCTTCATTTTTTGCAGCGTTTCTAAACGA
TTTCAACATTTTTAATTCAATCTCATCTTTGCACACTCTATGATAATTAG
AAAAGATTGCCAAACATCTATGTTGCAATTCTTTACTGCCTTGATTGCAA
TGCTTATCCAATTTTCTGTAGTCACTATCGCAATTCATGTCTAATATGGC
ATATTTCGCAACACAATATCTGTCAATTCTGTCTAACATTTTAATGCATT
TTCCGGTTCTTTCTCGGTAATTGCAAACTTTGTCATATTTTTCATAGTCA
GTATTGCAACGGGTGTCCAAATAAAAATATCTTCTTTCACAGACTTTGTC
ATGAGTTTCGAACTTAATTGCGCAATATTTATCAAGAGCCTTCCAATCTC
CGTCACAACTGATGACCTTTTTCAATAAATTTTGACATTCTTCATTATTT
CCAGAAATTGTTGAAATCGATATCCAGACAAAAATGACAAAATAAAGCAG
CATCACAATTGAATTTAATGCTAAAAAAATAGAAAACTTATTTTTATAAT
AAACTGAGTAGTAGTGGATACAGTAAACGGCTCAAACCTACATTCGCATT
AGCAGCACGCTTTTAATCAAATTGTACAATCTTACAAGTAGTAGTATGTT
TATTT
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protein sequence of SMED30011447-orf-1

>SMED30011447-orf-1 ID=SMED30011447-orf-1|Name=SMED30011447-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=192bp
MLLYFVIFVWISISTISGNNEECQNLLKKVISCDGDWKALDKYCAIKFET
HDKVCERRYFYLDTRCNTDYEKYDKVCNYRERTGKCIKMLDRIDRYCVAK
YAILDMNCDSDYRKLDKHCNQGSKELQHRCLAIFSNYHRVCKDEIELKML
KSFRNAAKNEEKTMKQTSKKEVKLVKKVVETKMSKTQTKTM*
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Aliases
The feature 'SMED30011447' has the following synonyms
Synonym
prog1-10
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000035Category 3 cell
PLANA:0002032epidermal cell
PLANA:0002142parenchyma
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 150..170
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.771