SMED30001010

Overview
NameSMED30001010
Smed IDSMED30001010
Length (bp)888
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 SMED30001010 (SMED30001010) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001010 (SMED30001010) 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 SMED30001010 (SMED30001010) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001010 (SMED30001010) 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



SMED30001010

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
head regionSMED30001010SMESG000039006.1 SmedASXL_008831SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30001010SMESG000039006.1 dd_Smed_v4_13470_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001010SMESG000039006.1 dd_Smed_v4_13470_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30001010SMESG000039006.1 dd_Smed_v4_13470_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30001010SMESG000039006.1 dd_Smed_v4_13470_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30001010SMESG000039006.1 dd_Smed_v4_13470_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001010SMESG000039006.1 Contig39726newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001010SMESG000039006.1 Contig39726uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30001010SMESG000039006.1 dd_Smed_v6_13470_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30001010SMESG000039006.1 OX_Smed_1.0.22665ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001010 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000424:95138..96067 +4338
Homology
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BLAST of SMED30001010 vs. TrEMBL
Match: V3ZQT2 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_166990 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 1.113e-7
Identity = 28/58 (48.28%), Postives = 40/58 (68.97%), Query Frame = 2 
Query:  263 YDPKGAGIYVSAVIFIWGLCIALLIASTIRKNRMDKTISLYLKEIQSIRHNSDKQKIL 436
            YD  GA  YV AV+ I+GL I ++IAS IRKN+ D  + +YLKE+  +R N  ++KI+
Sbjct:   40 YDESGALFYVVAVVMIYGLSIVMMIASHIRKNKQDSHLRIYLKEMAVLRKNDRREKIM 97
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BLAST of SMED30001010 vs. TrEMBL
Match: A0A2C9KT45 (Uncharacterized protein OS=Biomphalaria glabrata OX=6526 GN=106059450 PE=4 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 3.955e-7
Identity = 36/90 (40.00%), Postives = 52/90 (57.78%), Query Frame = 2 
Query:  266 DPKGAGIYVSAVIFIWGLCIALLIASTIRKNRMDKTISLYLKEIQSIRHNSDKQKILRLMPVDKSPKEKVRELLSRAISTEICEKEPTKS 535
            D  GA  YV AVIFI+GL I ++IAS IRKN+ D  +  YLKE+ ++R +  ++K+L           K+ +L +R    E  E + TKS
Sbjct:   86 DDIGALYYVVAVIFIYGLSIVMMIASHIRKNKQDSQLRTYLKEMANLRKSDRREKVL----------SKMNDLANRRKKQEAMEAKKTKS 165
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BLAST of SMED30001010 vs. TrEMBL
Match: A0A210QJE8 (Uncharacterized protein OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT08773 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 1.392e-6
Identity = 26/57 (45.61%), Postives = 39/57 (68.42%), Query Frame = 2 
Query:  266 DPKGAGIYVSAVIFIWGLCIALLIASTIRKNRMDKTISLYLKEIQSIRHNSDKQKIL 436
            D  GA  YV AV+FI+G  I ++IAS IRKN+ D  + +YLKE+  +R N  ++K++
Sbjct:   47 DDIGALYYVVAVVFIYGFSIVMMIASHIRKNKQDNQLRVYLKEMALLRKNDRREKLV 103
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BLAST of SMED30001010 vs. TrEMBL
Match: A0A433TCA8 (Uncharacterized protein OS=Elysia chlorotica OX=188477 GN=EGW08_012972 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 4.581e-6
Identity = 29/60 (48.33%), Postives = 40/60 (66.67%), Query Frame = 2 
Query:  266 DPKGAGIYVSAVIFIWGLCIALLIASTIRKNRMDKTISLYLKEIQSIRHNSDKQKILRLM 445
            D  GA  YV AVIFI+GL I ++IAS IRKN+ D  +  YLKE+ ++R    ++K+L  M
Sbjct:   72 DDIGALYYVVAVIFIYGLSIVMMIASHIRKNKQDSQLRTYLKEMSNLRKTERREKVLHKM 131
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BLAST of SMED30001010 vs. Planmine SMEST
Match: SMESG000039006.1 (SMESG000039006.1)

HSP 1 Score: 346.28 bits (887), Expect = 3.052e-121
Identity = 213/213 (100.00%), Postives = 213/213 (100.00%), Query Frame = 2 
Query:   89 MWVHHTLHQLLLSKDKFRLKLESINGSANYLLVSILSNDPQADSLSPEQLERKQFMINYDPKGAGIYVSAVIFIWGLCIALLIASTIRKNRMDKTISLYLKEIQSIRHNSDKQKILRLMPVDKSPKEKVRELLSRAISTEICEKEPTKSTLPSSINAFKLFRSKENAAXXXXXXXXXXXXXXXXXXNRXXXXXXXXDKSENTNLNGNNDNKVA 727
            MWVHHTLHQLLLSKDKFRLKLESINGSANYLLVSILSNDPQADSLSPEQLERKQFMINYDPKGAGIYVSAVIFIWGLCIALLIASTIRKNRMDKTISLYLKEIQSIRHNSDKQKILRLMPVDKSPKEKVRELLSRAISTEICEKEPTKSTLPSSINAFKLFRSKENAAKKPMIIPKICIDKDIDEDNRSGGSSESGDKSENTNLNGNNDNKVA
Sbjct:    1 MWVHHTLHQLLLSKDKFRLKLESINGSANYLLVSILSNDPQADSLSPEQLERKQFMINYDPKGAGIYVSAVIFIWGLCIALLIASTIRKNRMDKTISLYLKEIQSIRHNSDKQKILRLMPVDKSPKEKVRELLSRAISTEICEKEPTKSTLPSSINAFKLFRSKENAAKKPMIIPKICIDKDIDEDNRSGGSSESGDKSENTNLNGNNDNKVA 213
[Close]
BLAST of SMED30001010 vs. Planmine SMEST
Match: SMESG000046965.1 (SMESG000046965.1)

HSP 1 Score: 87.8113 bits (216), Expect = 1.006e-20
Identity = 39/60 (65.00%), Postives = 52/60 (86.67%), Query Frame = 2 
Query:  266 DPKGAGIYVSAVIFIWGLCIALLIASTIRKNRMDKTISLYLKEIQSIRHNSDKQKILRLM 445
            D +GA +YV AVI +WGL I LLIAST+RKNR+DK +SLYLKEIQ++R+ SD+QKIL+++
Sbjct:   47 DHQGAFMYVVAVILLWGLSIVLLIASTVRKNRLDKNVSLYLKEIQAVRNRSDRQKILQVV 106
The following BLAST results are available for this feature:
BLAST of SMED30001010 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 SMED30001010 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 SMED30001010 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 SMED30001010 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 SMED30001010 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 SMED30001010 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 SMED30001010 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 SMED30001010 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
V3ZQT21.113e-748.28Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
A0A2C9KT453.955e-740.00Uncharacterized protein OS=Biomphalaria glabrata O... [more]
A0A210QJE81.392e-645.61Uncharacterized protein OS=Mizuhopecten yessoensis... [more]
A0A433TCA84.581e-648.33Uncharacterized protein OS=Elysia chlorotica OX=18... [more]
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BLAST of SMED30001010 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 SMED30001010 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 SMED30001010 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 SMED30001010 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 SMED30001010 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 SMED30001010 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000039006.13.052e-121100.00SMESG000039006.1[more]
SMESG000046965.11.006e-2065.00SMESG000046965.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001010 ID=SMED30001010|Name=SMED30001010|organism=Schmidtea mediterranea sexual|type=transcript|length=888bp
GGAATTGAGGATGAGAAAATCTCGATTTTGATAGGCTGAAGGAATGCCAT
TCATTATTTTTCTTTTGCAAATTTTTTACAGCCGTACAATGTGGGTCCAT
CACACCCTTCATCAACTTCTTTTGAGCAAGGATAAATTCCGTTTAAAATT
GGAATCAATTAACGGGTCCGCAAATTATCTTTTAGTGTCGATTCTAAGCA
ATGATCCTCAAGCCGATTCTTTGTCTCCTGAACAACTGGAACGCAAGCAG
TTCATGATCAACTATGATCCTAAAGGGGCTGGAATTTATGTGTCAGCTGT
GATTTTTATCTGGGGATTATGCATCGCTTTGTTAATCGCGTCGACAATAC
GCAAAAACCGAATGGACAAAACGATTTCTCTGTATTTGAAAGAAATACAA
AGCATCCGGCACAATTCAGACAAGCAGAAAATTCTTCGATTAATGCCAGT
TGATAAAAGCCCAAAAGAAAAGGTAAGAGAATTGCTGTCGAGAGCAATTT
CCACAGAAATCTGTGAGAAAGAACCTACGAAAAGTACTTTACCAAGTTCA
ATTAATGCATTCAAGTTGTTTCGTTCGAAAGAGAATGCCGCTAAAAAACC
AATGATTATACCAAAAATATGTATAGATAAAGACATCGATGAAGATAATA
GAAGCGGCGGAAGTTCAGAATCAGGAGACAAATCGGAGAATACTAATCTC
AACGGAAATAATGATAACAAAGTTGCATGAAAAAAGAAAACTGTCGAGTT
TTATTAATTTGAATACATTTTAGGGGTATACCAACGATCTTGATGAGTGA
AATATTATTGCAATTACTTTCAGAAGTCTTTCTGAAATTATATTCAAAAA
TGATGAAATATTTTAATTAATAAATTCACAGCAAAATT
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protein sequence of SMED30001010-orf-1

>SMED30001010-orf-1 ID=SMED30001010-orf-1|Name=SMED30001010-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=229bp
MPFIIFLLQIFYSRTMWVHHTLHQLLLSKDKFRLKLESINGSANYLLVSI
LSNDPQADSLSPEQLERKQFMINYDPKGAGIYVSAVIFIWGLCIALLIAS
TIRKNRMDKTISLYLKEIQSIRHNSDKQKILRLMPVDKSPKEKVRELLSR
AISTEICEKEPTKSTLPSSINAFKLFRSKENAAKKPMIIPKICIDKDIDE
DNRSGGSSESGDKSENTNLNGNNDNKVA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 199..228
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 209..228
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..15
score: 0.452
NoneNo IPR availableTMHMMTMhelixcoord: 78..100