SMED30010097

Overview
NameSMED30010097
Smed IDSMED30010097
Length (bp)1467
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 SMED30010097 (SMED30010097) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010097 (SMED30010097) 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 SMED30010097 (SMED30010097) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010097 (SMED30010097) 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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Alignments
SMED30010097 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.015246:5943..7444 +5727
Homology
BLAST of SMED30010097 vs. TrEMBL
Match: A0A1I8I9B1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 1.581e-9
Identity = 39/163 (23.93%), Postives = 77/163 (47.24%), Query Frame = 2
Query:  413 RIMHNLAQWKFPTCLYIMFLSSLDLLSNTVKLLDKWCQITFSAKFLNSLVLTSHALCSTFTITIYLISHMISLVRSALSIDTYYSYINPLSNTRKIVVTRIXXXXXXXXXXXXXXNSHFLWTYSIIHMNNKQTSVPPGNYCTYIVKW-VNPTFRDVLWPLVDF 898
            R+M   ++ + P CLY+  L+ LD     ++ LD W Q  F  K L +L +   + C    +    + H  + ++ +L++DT      P+S   +     + + ++L   L+L+ N H LWT +++ ++          YC + ++W +   F   +WP+ D 
Sbjct: 2082 RLMLMYSKRQLPVCLYLALLAGLDTAMLWLRFLDLWLQAAFDIKLLLTLAIMDESTCQLINMLYSTLLHFKAALQVSLALDTVRMIRQPVSRIERYTAEWVKNSVILAFVLVLLLNGHHLWTLAVVKVSGGSGDAEGAFYCGWTLRWPITEQFAVWIWPISDL 2244          
BLAST of SMED30010097 vs. TrEMBL
Match: A0A1I8IH75 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.360e-8
Identity = 40/163 (24.54%), Postives = 77/163 (47.24%), Query Frame = 2
Query:  413 RIMHNLAQWKFPTCLYIMFLSSLDLLSNTVKLLDKWCQITFSAKFLNSLVLTSHALCSTFTITIYLISHMISLVRSALSIDTYYSYINPLSNTRKIVVTRIXXXXXXXXXXXXXXNSHFLWTYSIIHMNNKQTSVPPGNYCTYIVKW-VNPTFRDVLWPLVDF 898
            R+M   ++ + P CLY+  L+ LD     ++ LD W Q  F  K L +L +   + C    +    +  + + ++ +L+IDT      P+S   +     + + ++L   L+L+ N H LWT +++ +N+         YC +  +W +   F   +WP+ D 
Sbjct:   52 RMMLVYSRRQLPVCLYLALLAGLDTALLWLRFLDLWLQAAFDIKLLLTLAVMDESTCQLLNMLYSTLLQLKAGIQVSLAIDTTRLIRQPVSQLHRYTSEWVKNSVILAFVLVLLLNGHHLWTLTVVKVNSVPGEAEGALYCGWTQRWPITEQFAVWIWPISDL 214          
BLAST of SMED30010097 vs. TrEMBL
Match: A0A1I8I2J4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 5.652e-7
Identity = 40/163 (24.54%), Postives = 77/163 (47.24%), Query Frame = 2
Query:  413 RIMHNLAQWKFPTCLYIMFLSSLDLLSNTVKLLDKWCQITFSAKFLNSLVLTSHALCSTFTITIYLISHMISLVRSALSIDTYYSYINPLSNTRKIVVTRIXXXXXXXXXXXXXXNSHFLWTYSIIHMNNKQTSVPPGNYCTYIVKW-VNPTFRDVLWPLVDF 898
            R+M   ++ + P CLY+  L+ LD     ++ LD W Q  F  K L +L +   + C    +    +  + + ++ +L+IDT      P+S   +     + + ++L   L+L+ N H LWT +++ +N+         YC +  +W +   F   +WP+ D 
Sbjct:  320 RMMLVYSRRQLPVCLYLALLAGLDTALLWLRFLDLWLQAAFDIKLLLTLAVMDESTCQLLNMLYSTLLQLKAGIQVSLAIDTTRLIRQPVSQLHRYTSEWVKNSVILAFVLVLLLNGHHLWTLTVVKVNSVPGEAEGALYCGWTQRWPITEQFAVWIWPISDL 482          
BLAST of SMED30010097 vs. Planmine SMEST
Match: SMESG000039629.1 (SMESG000039629.1)

HSP 1 Score: 673.315 bits (1736), Expect = 0.000e+0
Identity = 406/409 (99.27%), Postives = 407/409 (99.51%), Query Frame = 2
Query:  158 MASVQSPVTTEDSKTPWHHSWIINSPKHTSKQDKPEREIIAFTTAFELDIEQIVNYELGNGLKETLRWLLPXXXXXXXXXXXXXXRIMHNLAQWKFPTCLYIMFLSSLDLLSNTVKLLDKWCQITFSAKFLNSLVLTSHALCSTFTITIYLISHMISLVRSALSIDTYYSYINPLSNTRKIVVTRIXXXXXXXXXXXXXXNSHFLWTYSIIHMNNKQTSVPPGNYCTYIVKWVNPTFRDVLWPLVDFXXXXXXXXXXXXXXXXXXXXXXXKHSCCTENSFSIENKKLSHYLIDVKTFMEMRKVXXXXXXXXXXXXXXPNAFSIIYKSIRYQLNHNMKMVTTFSIVRSTNRSYINPLDISILDIFVQILAAIFSVGSLVTCCILSPNGFMKEFKAIFLLTKKTSKINYQI 1384
            MASVQSPVTTEDSKTPWHHSWIINSPKHTSKQDKPEREIIAFTTAFEL+IEQIVNYELGNGLKETLRWLLPIIILCSITTNIIMIRIMHNLAQWKFP CLYIMFLSSLDLLSNTVKLLDKWCQITFSAKFLNSLVLTSHALCSTFTITIYLISHMISLVRSALSIDTYYSYINPLSNTRKIVVTRIHHLILLFTTLLLIFNSHFLWTYSIIHMNNKQTSVPPGNYCTYIVKWVNPTFRDVLWPLVDFSIGELCPIICIIISTILILICLSKHSCCTENSFSIENKKLSHYLIDVKTFMEMRKVILSYNILTLLLILIPNAFSIIYKSIRYQLNHNMKMVTTFSIVRSTNRSYINPLDISILDIFVQILAAIFSV SLVTCCILSPNGFMKEFKAIFLLTKKTSKINYQI
Sbjct:    1 MASVQSPVTTEDSKTPWHHSWIINSPKHTSKQDKPEREIIAFTTAFELEIEQIVNYELGNGLKETLRWLLPIIILCSITTNIIMIRIMHNLAQWKFPMCLYIMFLSSLDLLSNTVKLLDKWCQITFSAKFLNSLVLTSHALCSTFTITIYLISHMISLVRSALSIDTYYSYINPLSNTRKIVVTRIHHLILLFTTLLLIFNSHFLWTYSIIHMNNKQTSVPPGNYCTYIVKWVNPTFRDVLWPLVDFSIGELCPIICIIISTILILICLSKHSCCTENSFSIENKKLSHYLIDVKTFMEMRKVILSYNILTLLLILIPNAFSIIYKSIRYQLNHNMKMVTTFSIVRSTNRSYINPLDISILDIFVQILAAIFSVSSLVTCCILSPNGFMKEFKAIFLLTKKTSKINYQI 409          
The following BLAST results are available for this feature:
BLAST of SMED30010097 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 SMED30010097 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 SMED30010097 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 SMED30010097 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 SMED30010097 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 SMED30010097 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 SMED30010097 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 SMED30010097 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A1I8I9B11.581e-923.93Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8IH751.360e-824.54Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8I2J45.652e-724.54Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30010097 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 SMED30010097 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 SMED30010097 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 SMED30010097 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 SMED30010097 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 SMED30010097 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000039629.10.000e+099.27SMESG000039629.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010097 ID=SMED30010097|Name=SMED30010097|organism=Schmidtea mediterranea sexual|type=transcript|length=1467bp
TTCCCAGGTTATCTTCGGTAGTTATTTAATTGGTTCAATGAAAAAGGAAG
TCATTAATTATCAGAAATAATTGCTTATAAAATTCTGACCAATCAAATGT
CAGCTTGATCAATCTTAAATTGGAAATATCTCATCGCTAATCAGAAATTT
GATTCAAATGGCATCAGTTCAATCACCAGTAACGACTGAGGATTCAAAGA
CTCCTTGGCATCATTCATGGATCATTAATTCTCCAAAACATACTTCAAAA
CAAGACAAGCCTGAAAGAGAGATTATTGCATTTACAACAGCCTTTGAATT
GGACATTGAACAGATCGTGAATTATGAATTAGGTAACGGACTCAAGGAAA
CCTTAAGATGGCTACTTCCGATTATTATTCTGTGTTCTATAACCACAAAT
ATAATTATGATTCGAATCATGCACAATCTTGCACAATGGAAATTCCCAAC
GTGTCTTTATATAATGTTTTTATCCAGCCTTGATCTTTTAAGCAACACCG
TAAAATTGTTAGACAAATGGTGTCAAATCACATTTTCTGCTAAATTTTTG
AATTCTTTGGTGTTAACAAGTCATGCTCTATGCTCAACATTTACAATTAC
AATATACCTCATTTCTCATATGATCAGTCTAGTCAGATCAGCTCTTTCAA
TCGACACGTACTATTCTTACATAAACCCTTTATCGAATACAAGAAAAATT
GTAGTAACAAGAATCCATCATTTAATTCTCTTGTTTACAACATTACTACT
CATATTTAACAGTCATTTTTTGTGGACATATTCAATTATCCACATGAACA
ACAAACAAACCTCAGTACCTCCTGGAAACTATTGCACGTACATTGTAAAA
TGGGTCAATCCAACTTTCAGAGATGTTTTGTGGCCATTAGTCGACTTCTC
AATTGGTGAACTCTGTCCAATAATCTGCATAATAATTAGTACAATACTGA
TATTGATATGCCTGTCAAAACATTCATGTTGCACGGAAAATTCATTTTCC
ATTGAAAACAAAAAACTAAGTCATTATTTGATAGATGTAAAAACCTTCAT
GGAAATGAGAAAGGTTATTTTGTCATATAACATTCTCACCCTGCTTCTCA
TCCTAATACCAAATGCTTTTTCGATTATTTATAAAAGTATAAGATACCAA
TTAAACCATAACATGAAGATGGTGACTACATTCAGTATAGTAAGAAGCAC
AAACCGATCTTATATCAATCCACTAGATATTTCTATTCTAGATATTTTTG
TCCAAATACTCGCTGCTATATTCTCGGTCGGCTCACTAGTGACATGCTGC
ATTCTCTCGCCAAATGGATTCATGAAAGAATTCAAAGCCATATTTTTATT
AACAAAGAAAACATCAAAAATCAACTATCAAATTTAAAAATATTTATTCT
ATTACAATTTTATTATTCCAATTATATAAAATAATTTAAAATTAACATAT
ATAAATATAACGGGCGG
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protein sequence of SMED30010097-orf-1

>SMED30010097-orf-1 ID=SMED30010097-orf-1|Name=SMED30010097-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=410bp
MASVQSPVTTEDSKTPWHHSWIINSPKHTSKQDKPEREIIAFTTAFELDI
EQIVNYELGNGLKETLRWLLPIIILCSITTNIIMIRIMHNLAQWKFPTCL
YIMFLSSLDLLSNTVKLLDKWCQITFSAKFLNSLVLTSHALCSTFTITIY
LISHMISLVRSALSIDTYYSYINPLSNTRKIVVTRIHHLILLFTTLLLIF
NSHFLWTYSIIHMNNKQTSVPPGNYCTYIVKWVNPTFRDVLWPLVDFSIG
ELCPIICIIISTILILICLSKHSCCTENSFSIENKKLSHYLIDVKTFMEM
RKVILSYNILTLLLILIPNAFSIIYKSIRYQLNHNMKMVTTFSIVRSTNR
SYINPLDISILDIFVQILAAIFSVGSLVTCCILSPNGFMKEFKAIFLLTK
KTSKINYQI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR017452GPCR_Rhodpsn_7TM
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 63..405
e-value: 4.8E-9
score: 37.5
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 63..356
NoneNo IPR availableTMHMMTMhelixcoord: 363..385
NoneNo IPR availableTMHMMTMhelixcoord: 136..158
NoneNo IPR availableTMHMMTMhelixcoord: 303..325
NoneNo IPR availableTMHMMTMhelixcoord: 66..88
NoneNo IPR availableTMHMMTMhelixcoord: 247..269
NoneNo IPR availableTMHMMTMhelixcoord: 189..211
IPR017452GPCR, rhodopsin-like, 7TMPROSITEPS50262G_PROTEIN_RECEP_F1_2coord: 80..358
score: 9.8