SMED30020810

Overview
NameSMED30020810
Smed IDSMED30020810
Length (bp)494
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 SMED30020810 (SMED30020810) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020810 (SMED30020810) 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 SMED30020810 (SMED30020810) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020810 (SMED30020810) 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



SMED30020810

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30020810 dd_Smed_v4_6797_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30020810SMESG000068262.1 SMESG000053435.1 SMESG000049288.1 dd_Smed_v6_6797_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30020810 vs. TrEMBL
Match: A0A2B4SIV5 (Uncharacterized protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene6913 PE=4 SV=1)

HSP 1 Score: 76.2554 bits (186), Expect = 4.519e-13
Identity = 45/117 (38.46%), Postives = 68/117 (58.12%), Query Frame = -2 
Query:  128 VYKQIKGQPMSSFISGLLEICIFMDNHERQILRTLQSIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIE----YSDENG-SLNLLDLRIKIDVD-TSTYRFYKKPAAKK 460
            V +Q +G PM S ISG+L I +FMD  E   L +   I  Y RYVDDI++   +++  +  +H+ N  H +++FE E        NG SL+LLD ++ I  D  S++ FY++PA K 
Sbjct:  197 VLRQREGLPMGSNISGILAI-LFMDKLESIALTSHLMISPYKRYVDDIYLQTTNEETADHFHHVINNLHPNLRFENEKLKNQKTPNGMSLSLLDFKVTISKDGNSSFEFYQRPAKKP 312
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BLAST of SMED30020810 vs. TrEMBL
Match: A0A3L8DGL8 (Reverse transcriptase domain-containing protein OS=Ooceraea biroi OX=2015173 GN=DMN91_008131 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 1.495e-11
Identity = 46/110 (41.82%), Postives = 65/110 (59.09%), Query Frame = -2 
Query:  137 HVYKQIKGQPMSSFISGLLEICIFMDNHERQILRTLQ-SIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLDLRIKIDVDTSTYRFYKKPA 463
             +Y+QI G PM S +S +L   I +++ E Q L  L  +I +Y RYVDDIF MI +K  +   + IFN+ H  +KF  E  +ENGS++ LD RI  D  T    +Y+KP 
Sbjct:  203 QIYEQIFGSPMGSPLSPILA-DIVLEDLELQCLSDLDFTIPIYYRYVDDIF-MIIAKDKLMTTFDIFNSYHPRLKFTYEV-EENGSISFLDTRITNDNGTIITNWYRKPT 309
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BLAST of SMED30020810 vs. TrEMBL
Match: A0A016UVR2 (Reverse transcriptase domain-containing protein OS=Ancylostoma ceylanicum OX=53326 GN=Acey_s0026.g1425 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 2.757e-11
Identity = 41/113 (36.28%), Postives = 67/113 (59.29%), Query Frame = -2 
Query:  122 VYKQIKGQPMSSFISGLLEICIFMDNHERQILRTLQSIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLDLRIKIDVDTSTYRFYKKPAAKKNL 460
            VY+QI+G  M S I+ LL I IF+D+ E++ LR  + I  Y RY+DDIFI+ +S+  + +     N+A+ +I F +E   E+  L  L+ +++I        +YK+PA+   L
Sbjct:  123 VYRQIRGLAMGSRIAPLLAI-IFLDSIEKRALR--RGIIYYKRYIDDIFIVARSRCSLRKTLQNLNSANDNITFTVEDPGEDNFLPFLNTKVRIRSGKVESIWYKEPASANVL 232
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BLAST of SMED30020810 vs. TrEMBL
Match: A0A016W357 (Reverse transcriptase domain-containing protein OS=Ancylostoma ceylanicum OX=53326 GN=Acey_s0001.g341 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 3.160e-11
Identity = 42/113 (37.17%), Postives = 67/113 (59.29%), Query Frame = -2 
Query:  122 VYKQIKGQPMSSFISGLLEICIFMDNHERQILRTLQSIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLDLRIKIDVDTSTYRFYKKPAAKKNL 460
            +++Q +G  M + I+ LL I IF+D+ ER  L +   I LY RY+DD+F++   K  VE+     NT   +I F IE  D++G L  L+ +I+I    + Y +Y+KPA++  L
Sbjct:  181 IFEQRRGLAMGNRIAPLLAI-IFLDHIERMSLTS--EILLYKRYIDDVFVIGCDKTEVEKTLKRLNTFDDNISFTIEEPDDDGFLPFLNTKIRIVDGRTEYLWYRKPASRNIL 290
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BLAST of SMED30020810 vs. TrEMBL
Match: A0A016TGJ6 (Reverse transcriptase domain-containing protein OS=Ancylostoma ceylanicum OX=53326 GN=Acey_s0105.g3708 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 5.195e-11
Identity = 42/113 (37.17%), Postives = 67/113 (59.29%), Query Frame = -2 
Query:  122 VYKQIKGQPMSSFISGLLEICIFMDNHERQILRTLQSIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLDLRIKIDVDTSTYRFYKKPAAKKNL 460
            +++Q +G  M + I+ LL I IF+D+ ER  L +   I LY RY+DD+F++   K  VE+     NT   +I F IE  D++G L  L+ +I+I    + Y +Y+KPA++  L
Sbjct:  430 LFEQRRGLAMGNRIAPLLAI-IFLDHIERMSLTS--GILLYKRYIDDVFVIGCDKTEVEKTLKRLNTFDDNISFTIEEPDDDGFLPFLNTKIRIVDGRTEYLWYRKPASRNIL 539
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BLAST of SMED30020810 vs. Planmine SMEST
Match: SMESG000069853.1 (SMESG000069853.1)

HSP 1 Score: 133.65 bits (335), Expect = 2.363e-38
Identity = 63/87 (72.41%), Postives = 71/87 (81.61%), Query Frame = -2 
Query:  146 EICIFMDNHERQILRTLQSIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLDLRIKIDVDTSTYRFYK 406
            + CIF+DN ERQ LRT++SIG YARYVDDIFI  K  K  +EI+HI N AH +IKFEIEY DENGSLNLLDLRIKIDVDT T+ FYK
Sbjct:  121 QACIFIDNLERQTLRTIKSIGFYARYVDDIFITAKGIKDAKEIFHISNAAHPNIKFEIEYPDENGSLNLLDLRIKIDVDTPTFEFYK 207
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BLAST of SMED30020810 vs. Planmine SMEST
Match: SMESG000049225.1 (SMESG000049225.1)

HSP 1 Score: 113.62 bits (283), Expect = 3.217e-30
Identity = 56/79 (70.89%), Postives = 62/79 (78.48%), Query Frame = -2 
Query:  128 RTLQSIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLDLRIKIDVDTSTYRFYKKPAAKK 364
            RT+QSIG YARYVDDIFI  + KK  EEI+HIFN  H +IKFEIEY D NGSLNLLDLRIKIDVDT TY   KK A ++
Sbjct:  143 RTIQSIGFYARYVDDIFITTEIKKEAEEIFHIFNEDHPEIKFEIEYPDINGSLNLLDLRIKIDVDTPTYELCKKSAGEE 221
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BLAST of SMED30020810 vs. Planmine SMEST
Match: SMESG000039356.1 (SMESG000039356.1)

HSP 1 Score: 53.5286 bits (127), Expect = 1.200e-8
Identity = 35/108 (32.41%), Postives = 57/108 (52.78%), Query Frame = -2 
Query:  137 YKQIKGQPMSSFISGLLEICIFMDNHERQILR-TLQSIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLDLRIKIDVDTSTYRFYKKPA 457
            Y+QI G  M S ++  +   IF+ + E++I     +   +Y RYVDDIF++ +++K VE   H  N+ H +I F  E ++   S+  LDL I+          Y+KP 
Sbjct:  643 YQQIDGVAMGSPLAPTMA-SIFLASLEKKIASFQFKKPFVYKRYVDDIFLIFENQKHVEPFLHFMNSLHKNIVFTCE-TERKSSIAFLDLLIQRKDKQYETEIYRKPT 748
[Close]
BLAST of SMED30020810 vs. Planmine SMEST
Match: SMESG000060260.1 (SMESG000060260.1)

HSP 1 Score: 51.9878 bits (123), Expect = 3.919e-8
Identity = 32/93 (34.41%), Postives = 53/93 (56.99%), Query Frame = -2 
Query:  182 YKQIKGQPMSSFISGLLEICIFMDNHERQILR-TLQSIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLDLRIK 457
            Y+QI G  M S ++  +   IF+ + E++I     +   +Y RYVDDIF++ +++K VE   H  N+ H +I F  E ++   S+  LDL I+
Sbjct:  425 YQQIDGVAMGSPLAPTMA-SIFLASLEKKIASFQFEKPFVYKRYVDDIFLIFENQKHVEPFLHFMNSLHKNIVFTCE-TERKSSIAFLDLLIQ 515
[Close]
BLAST of SMED30020810 vs. Planmine SMEST
Match: SMESG000043973.1 (SMESG000043973.1)

HSP 1 Score: 51.6026 bits (122), Expect = 5.739e-8
Identity = 32/93 (34.41%), Postives = 53/93 (56.99%), Query Frame = -2 
Query:  182 YKQIKGQPMSSFISGLLEICIFMDNHERQILR-TLQSIGLYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLDLRIK 457
            Y+QI G  M S ++  +   IF+ + E++I     +   +Y RYVDDIF++ +++K VE   H  N+ H +I F  E ++   S+  LDL I+
Sbjct:   50 YQQIDGVAMGSPLAPTMA-SIFLASLEKKIASFQFEKPFVYKRYVDDIFLIFENQKHVEPFLHFMNSLHKNIVFTCE-TERKSSIAFLDLLIQ 140
The following BLAST results are available for this feature:
BLAST of SMED30020810 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 SMED30020810 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 SMED30020810 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 SMED30020810 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 SMED30020810 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 SMED30020810 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 SMED30020810 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 SMED30020810 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2B4SIV54.519e-1338.46Uncharacterized protein OS=Stylophora pistillata O... [more]
A0A3L8DGL81.495e-1141.82Reverse transcriptase domain-containing protein OS... [more]
A0A016UVR22.757e-1136.28Reverse transcriptase domain-containing protein OS... [more]
A0A016W3573.160e-1137.17Reverse transcriptase domain-containing protein OS... [more]
A0A016TGJ65.195e-1137.17Reverse transcriptase domain-containing protein OS... [more]
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BLAST of SMED30020810 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 SMED30020810 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 SMED30020810 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 SMED30020810 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 SMED30020810 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 SMED30020810 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000069853.12.363e-3872.41SMESG000069853.1[more]
SMESG000049225.13.217e-3070.89SMESG000049225.1[more]
SMESG000039356.11.200e-832.41SMESG000039356.1[more]
SMESG000060260.13.919e-834.41SMESG000060260.1[more]
SMESG000043973.15.739e-834.41SMESG000043973.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020810 ID=SMED30020810|Name=SMED30020810|organism=Schmidtea mediterranea sexual|type=transcript|length=494bp
ATCGAAATTTAGTTGTTGTTTATAGTTCTCTTTTTCTTCAAAACATCGAT
AAACTATCTTCTGCTTCTAGTTCTTTATAACATTTACTTTCTGTATATTT
GAAGTTATGATCTTTAAAACATAAATTTTTCTTTGCGGCTGGTTTTTTGT
AGAATCTGTAGGTTGACGTGTCTACATCTATTTTGATTCTTAAATCTAGT
AGATTGAGGGATCCATTTTCATCCGAGTACTCTATTTCAAACTTGATATC
CGAATGAGCCGTATTGAATATATGATATATTTCTTCCACTCCTTTCTTGC
TCTTGATCATGATAAATATATCATCTACATATCTTGCGTATAGACCAATA
GATTGTAGGGTCCTCAGTATCTGTCGTTCGTGGTTATCCATAAATATGCA
GATCTCTAGCAAGCCTGATATGAAAGAGCTCATTGGCTGACCTTTAATTT
GTTTATATACATGTATCCCCTGTATAACGCGGTAGTTACGTTCC
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protein sequence of SMED30020810-orf-1

>SMED30020810-orf-1 ID=SMED30020810-orf-1|Name=SMED30020810-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=152bp
ERNYRVIQGIHVYKQIKGQPMSSFISGLLEICIFMDNHERQILRTLQSIG
LYARYVDDIFIMIKSKKGVEEIYHIFNTAHSDIKFEIEYSDENGSLNLLD
LRIKIDVDTSTYRFYKKPAAKKNLCFKDHNFKYTESKCYKELEAEDSLSM
F*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0002032epidermal cell