SMED30024819

Overview
NameSMED30024819
Smed IDSMED30024819
Length (bp)1602
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 SMED30024819 (SMED30024819) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024819 (SMED30024819) 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 SMED30024819 (SMED30024819) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024819 (SMED30024819) 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
SMED30024819 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001369:31942..33796 -7810
Homology
BLAST of SMED30024819 vs. Planmine SMEST
Match: SMESG000066939.1 (SMESG000066939.1)

HSP 1 Score: 487.649 bits (1254), Expect = 1.871e-172
Identity = 262/262 (100.00%), Postives = 262/262 (100.00%), Query Frame = 2
Query:   74 MKLIPSESGLANSVEKREFSIENACHKLPKYMTNSVPDENYDNENKHREICLWKMPNNLRNSEITNYVTNLKKKGYREDQALLALQCNNYNVTSAIGDICQYRPKIGLFELNVIETADKISKIMIXXXXXXXXXXXCFRQIHNKFPNYTMGELLHFYMSNKLKVKRRLAKYKKQFEKLSKIPSEEEYERIINKLKCADENLLXXXXXXXXXXXXIWSRQEVYSFFQALGMFGENFVMISQFIGNKSESMVKLFYAQNVKNAM 859
            MKLIPSESGLANSVEKREFSIENACHKLPKYMTNSVPDENYDNENKHREICLWKMPNNLRNSEITNYVTNLKKKGYREDQALLALQCNNYNVTSAIGDICQYRPKIGLFELNVIETADKISKIMINNRKNNQNRKRCFRQIHNKFPNYTMGELLHFYMSNKLKVKRRLAKYKKQFEKLSKIPSEEEYERIINKLKCADENLLDSDSSMKSESDEIWSRQEVYSFFQALGMFGENFVMISQFIGNKSESMVKLFYAQNVKNAM
Sbjct:    1 MKLIPSESGLANSVEKREFSIENACHKLPKYMTNSVPDENYDNENKHREICLWKMPNNLRNSEITNYVTNLKKKGYREDQALLALQCNNYNVTSAIGDICQYRPKIGLFELNVIETADKISKIMINNRKNNQNRKRCFRQIHNKFPNYTMGELLHFYMSNKLKVKRRLAKYKKQFEKLSKIPSEEEYERIINKLKCADENLLDSDSSMKSESDEIWSRQEVYSFFQALGMFGENFVMISQFIGNKSESMVKLFYAQNVKNAM 262          
BLAST of SMED30024819 vs. Planmine SMEST
Match: SMESG000066939.1 (SMESG000066939.1)

HSP 1 Score: 390.193 bits (1001), Expect = 1.310e-134
Identity = 202/202 (100.00%), Postives = 202/202 (100.00%), Query Frame = 2
Query:   74 MKLIPSESGLANSVEKREFSIENACHKLPKYMTNSVPDENYDNENKHREICLWKMPNNLRNSEITNYVTNLKKKGYREDQALLALQCNNYNVTSAIGDICQYRPKIGLFELNVIETADKISKIMIXXXXXXXXXXXCFRQIHNKFPNYTMGELLHFYMSNKLKVKRRLAKYKKQFEKLSKIPSEEEYERIINKLKCADENLL 679
            MKLIPSESGLANSVEKREFSIENACHKLPKYMTNSVPDENYDNENKHREICLWKMPNNLRNSEITNYVTNLKKKGYREDQALLALQCNNYNVTSAIGDICQYRPKIGLFELNVIETADKISKIMINNRKNNQNRKRCFRQIHNKFPNYTMGELLHFYMSNKLKVKRRLAKYKKQFEKLSKIPSEEEYERIINKLKCADENLL
Sbjct:    1 MKLIPSESGLANSVEKREFSIENACHKLPKYMTNSVPDENYDNENKHREICLWKMPNNLRNSEITNYVTNLKKKGYREDQALLALQCNNYNVTSAIGDICQYRPKIGLFELNVIETADKISKIMINNRKNNQNRKRCFRQIHNKFPNYTMGELLHFYMSNKLKVKRRLAKYKKQFEKLSKIPSEEEYERIINKLKCADENLL 202          

HSP 2 Score: 53.1434 bits (126), Expect = 1.318e-7
Identity = 24/27 (88.89%), Postives = 27/27 (100.00%), Query Frame = 3
Query:  702 QNQMKFGVDKKCTVSFKPSECLVKILS 782
            +++MKFGVDKKCTVSFKPSECLVKILS
Sbjct:  209 KSEMKFGVDKKCTVSFKPSECLVKILS 235          
BLAST of SMED30024819 vs. Planmine SMEST
Match: SMESG000015035.1 (SMESG000015035.1)

HSP 1 Score: 61.6178 bits (148), Expect = 5.192e-10
Identity = 50/174 (28.74%), Postives = 88/174 (50.57%), Query Frame = 2
Query:  155 LPKYMTNSVPDENYDNENKHREICLWKMPNNLRNSEITNYVTNLKKKGYREDQALLALQCNNYNVTSAIGDICQYRPKIGLFELNVIETADKISKIMIXXXXXXXXXXXCFRQ----IHNKFPNYTMGELLHFYMSNKLKVKRRLAKYKKQFEKLSKIPSEEEYERIINKLKCA 664
            +PK+    +P ENY N    RE  +WK    L + + + ++    +KG+ E+QAL  ++ NN+++T +  D+  Y+P      LN + T      I +        +   F +    I ++FP +TMGELL FY +N++ +KR+  K K + + + +  +  +Y   IN L C 
Sbjct:   35 IPKFKRLCMPLENYQN---CRETLIWKEDEYLSD-KTSEFIKFAIEKGFTEEQALHIIKFNNFDLTLSECDLEIYKP------LNGMRTNQNRDIIKMIIETIKARKSNRFNRDLNLILSEFPAHTMGELLDFYANNRMSIKRKTVKCKSESKGIKR-KNVVDYLSQINPLLCG 197          
BLAST of SMED30024819 vs. Planmine SMEST
Match: SMESG000030733.1 (SMESG000030733.1)

HSP 1 Score: 48.9062 bits (115), Expect = 5.584e-7
Identity = 34/112 (30.36%), Postives = 66/112 (58.93%), Query Frame = 2
Query:  545 MSNKLKVKRRLAKYKKQFEKLSKIPSEEEYERIINKLKCAD---ENLLXXXXXXXX--------XXXXIWSRQEVYSFFQALGMFGENFVMISQFIGNKSESMVKLFYAQNV 847
            M NKLK+KR++AK K++++KL  +P+E E++ II+++K  +   E +L+ DS            + DE W+ ++       L  +G ++  ++  +G K+++M+K F  Q+V
Sbjct:    1 MRNKLKIKRKVAKEKRKYKKLHFLPTESEFQSIIDRIKPDNYECEPILNDDSDDDDCVIIKEFNQIDEDWTTRDCALLCLGLNDYGYDYSKLAIRVGTKTDAMIKNFIQQHV 112          
The following BLAST results are available for this feature:
BLAST of SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 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 SMED30024819 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000066939.11.871e-172100.00SMESG000066939.1[more]
SMESG000066939.11.310e-134100.00SMESG000066939.1[more]
SMESG000015035.15.192e-1028.74SMESG000015035.1[more]
SMESG000030733.15.584e-730.36SMESG000030733.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024819 ID=SMED30024819|Name=SMED30024819|organism=Schmidtea mediterranea sexual|type=transcript|length=1602bp
TGAAAAATGTTTGTTTAAATTTATTGCAATTCTCAATTTATTTTAAAGTT
TTTAAAATATATTTTATATTTTAATGAAATTAATCCCATCGGAATCTGGA
TTAGCTAATAGTGTTGAGAAAAGAGAATTCTCAATCGAAAATGCTTGCCA
TAAACTGCCTAAATATATGACAAATTCCGTCCCTGATGAAAATTATGACA
ATGAAAATAAACACAGAGAGATATGCTTATGGAAAATGCCTAATAATCTA
CGCAATTCAGAAATAACAAATTATGTCACCAATTTGAAAAAGAAAGGCTA
TCGGGAAGATCAAGCTCTTCTAGCGTTACAATGTAACAATTATAATGTCA
CATCAGCTATTGGGGATATCTGCCAATATCGTCCCAAAATCGGTTTATTT
GAATTAAACGTTATCGAAACCGCAGACAAAATCAGTAAAATTATGATAAA
TAACCGCAAAAATAACCAAAATCGGAAGCGCTGTTTTCGTCAAATTCACA
ATAAATTTCCGAATTACACAATGGGAGAATTGTTGCATTTCTATATGTCA
AACAAACTCAAAGTGAAACGTCGATTAGCCAAATACAAAAAGCAATTTGA
AAAACTCTCGAAAATCCCATCAGAAGAAGAATACGAACGAATAATCAACA
AGCTGAAATGTGCCGACGAAAACTTATTGGACAGCGATTCATCAATGAAA
TCAGAATCAGATGAAATTTGGAGTCGACAAGAAGTGTACAGTTTCTTTCA
AGCCCTCGGAATGTTTGGTGAAAATTTTGTCATGATTTCCCAGTTTATCG
GCAACAAATCCGAAAGCATGGTGAAATTGTTTTACGCTCAAAATGTCAAA
AATGCCATGTAGAAAATATTTTATAGATTTGTTTTTCTTTTTATTGAAAT
TAATGAGAGAAAAAAATGTTTTTTGTCATTCGTGGATTAATTGAAGATTA
TTTCATTGTTGTGAATGTTCTGTGTAAATTCTCTCTGCTACTCTAGATTT
GCTCAAATTATTCGAGTCTTATTGTAAATTGTACATTTATATATTTTCTA
AATTTAGTAACATGATTTGATTGGTTGTGGTTAAATCAATAAATTTTATA
GAGATTGCCATTATAATATATTTCTGTTGGAATTTTATACGTTCGAAATT
TGTATTTGTTTGTAAGATAATTATTTCCAAAGTTATTTTATCACAAAGTT
CTATCGTAAACATCGGGATATTTTTATGAAATCGGAAATCCATTTTATAT
AAATGATCATATTTGATGTTTGCTGATGTTTGATGAGTAACGTAAAAGAG
CGAGGCTGGACTGGCGTTACAAATGTTCTGTACAATATTCATATTTACTT
TTGTTTTATTATTTGTACGCAAAGTGGCCTTCATCGCAAATTTTATGAAA
TACAAATTTATTATGATTAATGATTGCCAGTAGGTTTTCATATTGCCTCG
AGGAGTTTTGACTTTTATTCAAGGTTTACTATAATAATGTGGAATTAACC
ATTGTTGTCAAAGAGATGTAACTCTAGAGGATTTATTTTACATCAATTTT
ATTTAAATAAATTTAATTATTTTTCTTGTTTGCTTTCATTAAAATATCGC
AT
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protein sequence of SMED30024819-orf-1

>SMED30024819-orf-1 ID=SMED30024819-orf-1|Name=SMED30024819-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=135bp
MKTYWQSLIIINLYFIKFAMKATLRTNNKTKVNMNIVQNICNASPASLFY
VTHQTSANIKYDHLYKMDFRFHKNIPMFTIELCDKITLEIIILQTNTNFE
RIKFQQKYIIMAISIKFIDLTTTNQIMLLNLENI*
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protein sequence of SMED30024819-orf-2

>SMED30024819-orf-2 ID=SMED30024819-orf-2|Name=SMED30024819-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=263bp
MKLIPSESGLANSVEKREFSIENACHKLPKYMTNSVPDENYDNENKHREI
CLWKMPNNLRNSEITNYVTNLKKKGYREDQALLALQCNNYNVTSAIGDIC
QYRPKIGLFELNVIETADKISKIMINNRKNNQNRKRCFRQIHNKFPNYTM
GELLHFYMSNKLKVKRRLAKYKKQFEKLSKIPSEEEYERIINKLKCADEN
LLDSDSSMKSESDEIWSRQEVYSFFQALGMFGENFVMISQFIGNKSESMV
KLFYAQNVKNAM*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002032epidermal cell
PLANA:0002089reproductive organ
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR001005SANT/Myb
IPR009060UBA-like_sf
IPR009057Homeobox-like_sf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0003677DNA binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001005SANT/Myb domainSMARTSM00717santcoord: 212..260
e-value: 0.0055
score: 25.9
IPR001005SANT/Myb domainCDDcd00167SANTcoord: 216..254
e-value: 0.00949016
score: 31.3918
NoneNo IPR availableGENE3DG3DSA:1.20.58.1880coord: 163..261
e-value: 2.4E-10
score: 42.6
IPR009060UBA-like superfamilySUPERFAMILYSSF46934UBA-likecoord: 43..101
IPR009057Homeobox-like domain superfamilySUPERFAMILYSSF46689Homeodomain-likecoord: 214..259