SMED30018799

Overview
NameSMED30018799
Smed IDSMED30018799
Length (bp)461
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 SMED30018799 (SMED30018799) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018799 (SMED30018799) 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 SMED30018799 (SMED30018799) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018799 (SMED30018799) 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.
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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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Homology
BLAST of SMED30018799 vs. Planmine SMEST
Match: SMESG000014348.1 (SMESG000014348.1)

HSP 1 Score: 116.316 bits (290), Expect = 6.591e-36
Identity = 53/66 (80.30%), Postives = 61/66 (92.42%), Query Frame = 1
Query:  157 IRDAIQISIKERMGKYWVEILPEVEFMLNVTIQKTTQLSHAQVVFGKKIARERYENDETCNMQLFM 354
            IRDA+QIS+KER GKY VEILPEV+FMLN TIQKTTQLS AQ++FGKKIARERYEND+TC++QL M
Sbjct:  214 IRDAVQISLKERTGKYCVEILPEVDFMLNATIQKTTQLSPAQIIFGKKIARERYENDKTCDLQLLM 279          

HSP 2 Score: 51.6026 bits (122), Expect = 6.591e-36
Identity = 26/32 (81.25%), Postives = 28/32 (87.50%), Query Frame = 3
Query:  366 KSERLELKKRIQGREETELLSEEKLPNRIFNV 461
            KSERLELKK I+GR+ETEL SEE  PNRIFNV
Sbjct:  283 KSERLELKKWIRGRKETELFSEEMQPNRIFNV 314          
BLAST of SMED30018799 vs. Planmine SMEST
Match: SMESG000046807.1 (SMESG000046807.1)

HSP 1 Score: 107.457 bits (267), Expect = 5.680e-34
Identity = 48/55 (87.27%), Postives = 52/55 (94.55%), Query Frame = 1
Query:  190 RMGKYWVEILPEVEFMLNVTIQKTTQLSHAQVVFGKKIARERYENDETCNMQLFM 354
            +MGK WVEILPEVEFMLN TIQKTTQLS AQ+VFGKKIARERYENDETC++QLFM
Sbjct:  118 KMGKDWVEILPEVEFMLNATIQKTTQLSPAQIVFGKKIARERYENDETCDLQLFM 172          

HSP 2 Score: 53.9138 bits (128), Expect = 5.680e-34
Identity = 27/31 (87.10%), Postives = 28/31 (90.32%), Query Frame = 3
Query:  366 KSERLELKKRIQGREETELLSEEKLPNRIFN 458
            KSERLELKKRIQGR+E EL SEEK PNRIFN
Sbjct:  176 KSERLELKKRIQGRKEVELFSEEKRPNRIFN 206          
BLAST of SMED30018799 vs. Planmine SMEST
Match: SMESG000037636.1 (SMESG000037636.1)

HSP 1 Score: 121.709 bits (304), Expect = 1.397e-32
Identity = 56/66 (84.85%), Postives = 61/66 (92.42%), Query Frame = 1
Query:  157 IRDAIQISIKERMGKYWVEILPEVEFMLNVTIQKTTQLSHAQVVFGKKIARERYENDETCNMQLFM 354
            IR+ I IS+KERMGK WVEILPEVEFMLN TIQKTTQLS AQ+VFGKKIARERYENDETC++QLFM
Sbjct: 1296 IRNGILISLKERMGKDWVEILPEVEFMLNATIQKTTQLSPAQIVFGKKIARERYENDETCDLQLFM 1361          
BLAST of SMED30018799 vs. Planmine SMEST
Match: SMESG000037636.1 (SMESG000037636.1)

HSP 1 Score: 121.709 bits (304), Expect = 1.474e-32
Identity = 56/66 (84.85%), Postives = 61/66 (92.42%), Query Frame = 1
Query:  157 IRDAIQISIKERMGKYWVEILPEVEFMLNVTIQKTTQLSHAQVVFGKKIARERYENDETCNMQLFM 354
            IR+ I IS+KERMGK WVEILPEVEFMLN TIQKTTQLS AQ+VFGKKIARERYENDETC++QLFM
Sbjct: 1404 IRNGILISLKERMGKDWVEILPEVEFMLNATIQKTTQLSPAQIVFGKKIARERYENDETCDLQLFM 1469          
BLAST of SMED30018799 vs. Planmine SMEST
Match: SMESG000037636.1 (SMESG000037636.1)

HSP 1 Score: 121.709 bits (304), Expect = 1.543e-32
Identity = 56/66 (84.85%), Postives = 61/66 (92.42%), Query Frame = 1
Query:  157 IRDAIQISIKERMGKYWVEILPEVEFMLNVTIQKTTQLSHAQVVFGKKIARERYENDETCNMQLFM 354
            IR+ I IS+KERMGK WVEILPEVEFMLN TIQKTTQLS AQ+VFGKKIARERYENDETC++QLFM
Sbjct: 1349 IRNGILISLKERMGKDWVEILPEVEFMLNATIQKTTQLSPAQIVFGKKIARERYENDETCDLQLFM 1414          
The following BLAST results are available for this feature:
BLAST of SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 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 SMED30018799 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014348.16.591e-3680.30SMESG000014348.1[more]
SMESG000046807.15.680e-3487.27SMESG000046807.1[more]
SMESG000037636.11.397e-3284.85SMESG000037636.1[more]
SMESG000037636.11.474e-3284.85SMESG000037636.1[more]
SMESG000037636.11.543e-3284.85SMESG000037636.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018799 ID=SMED30018799|Name=SMED30018799|organism=Schmidtea mediterranea sexual|type=transcript|length=461bp
GTTTATTTATTTGAATCGATTTTCATCGACTTTTGTGGCCCAATGAATAC
TTCTAGGAATGAAAAGAGATATACTTTGGCAATAATAGACCAATTTAGTA
AATATATTTCTTTGAGTGCAGCTTCTGGGCAAGATAAAAAGACAATTGCA
GCAATAATTAGAGATGCTATCCAGATCTCCATAAAAGAAAGAATGGGCAA
ATACTGGGTCGAAATACTTCCTGAAGTTGAATTTATGTTGAATGTGACAA
TTCAGAAAACTACTCAGTTGAGTCATGCACAAGTTGTTTTTGGGAAAAAG
ATTGCAAGAGAGCGGTACGAAAATGACGAAACGTGTAACATGCAATTATT
TATGGCAAAATTCTTAAATCCGAAAGATTAGAGTTAAAAAAGCGGATACA
AGGGAGAGAAGAAACTGAACTGCTTTCCGAAGAAAAACTACCAAACCGAA
TCTTCAATGTG
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protein sequence of SMED30018799-orf-1

>SMED30018799-orf-1 ID=SMED30018799-orf-1|Name=SMED30018799-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=127bp
VYLFESIFIDFCGPMNTSRNEKRYTLAIIDQFSKYISLSAASGQDKKTIA
AIIRDAIQISIKERMGKYWVEILPEVEFMLNVTIQKTTQLSHAQVVFGKK
IARERYENDETCNMQLFMAKFLNPKD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
Vocabulary: INTERPRO
TermDefinition
IPR012337RNaseH-like_sf
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
Vocabulary: biological process
TermDefinition
GO:0015074DNA integration