SMED30034100

Overview
NameSMED30034100
Smed IDSMED30034100
Length (bp)702
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 SMED30034100 (SMED30034100) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034100 (SMED30034100) 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 SMED30034100 (SMED30034100) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034100 (SMED30034100) 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
SMED30034100 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001338:24148..24827 +2327
Homology
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BLAST of SMED30034100 vs. Planmine SMEST
Match: SMESG000034928.1 (SMESG000034928.1)

HSP 1 Score: 79.7221 bits (195), Expect = 6.361e-22
Identity = 41/90 (45.56%), Postives = 56/90 (62.22%), Query Frame = 3 
Query:   21 RPTATAHALQIIGISKKGEYFKLKTVIQDMFNEKMQFGIHSTLEDVKCIRRIYLKIENQRVDYVNLAKKLPAKKYSLEEYRRFHENETIS 290
            R  ATA AL+ IG+ ++GE+FKLKTV+Q+MF ++M   IHS LEDV+ IR                  K P++KYSLEEYR+ H + + S
Sbjct: 1319 RDLATAQALEKIGMFRRGEFFKLKTVVQEMFGDQMWVAIHSALEDVRNIR------------------KQPSRKYSLEEYRKLHNSTSTS 1390

HSP 2 Score: 42.3578 bits (98), Expect = 6.361e-22
Identity = 30/73 (41.10%), Postives = 38/73 (52.05%), Query Frame = 1 
Query:  289 LQTTTSKGTIGILKE------------SETPTDQLKSLTELYLDPIEKNLVVIRNPVIQRIQVSFEYGPILYF 471
            L  +TS    GI +E             ET T QLK  TE  ++ IEK+L +I N  I RIQ  FE+GPI+ F
Sbjct: 1383 LHNSTSTSMTGITEEIDLTAAEDMETDGETQTVQLKWATEESIEIIEKSLGLIINEPIHRIQPIFEHGPIILF 1455
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BLAST of SMED30034100 vs. Planmine SMEST
Match: SMESG000058166.1 (SMESG000058166.1)

HSP 1 Score: 66.6254 bits (161), Expect = 1.031e-18
Identity = 34/45 (75.56%), Postives = 36/45 (80.00%), Query Frame = 3 
Query:  159 KCIRRIYLKIENQRVDYVNLAKKLPAKKYSLEEYRRFHENETISA 293
            KC  RIYLKIE + VD V + K LPAKKYSLEEYRRFH NETISA
Sbjct:  123 KC--RIYLKIEKKWVDNVKIPKMLPAKKYSLEEYRRFHGNETISA 165

HSP 2 Score: 35.8094 bits (81), Expect = 1.031e-18
Identity = 18/28 (64.29%), Postives = 20/28 (71.43%), Query Frame = 2 
Query:   29 SNSTRSADHWNIEKR*IL*VENGYPGYV 112
            +N T S DH NIEK  IL V+NGYPG V
Sbjct:   93 ANCTSSTDHGNIEKWRILQVKNGYPGSV 120

HSP 3 Score: 28.4906 bits (62), Expect = 1.031e-18
Identity = 13/16 (81.25%), Postives = 15/16 (93.75%), Query Frame = 1 
Query:  295 TTTSKGTIGILKESET 342
            TTTSKGT+GIL+ES T
Sbjct:  167 TTTSKGTVGILEESVT 182
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BLAST of SMED30034100 vs. Planmine SMEST
Match: SMESG000025296.1 (SMESG000025296.1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.016e-17
Identity = 36/69 (52.17%), Postives = 49/69 (71.01%), Query Frame = 3 
Query:   54 IGISKKGEYFKLKTVIQDMFNEKMQFGIHSTLEDVKCIRRIYLKIENQRVDYVNLAKKLPAKKYSLEEY 260
            +GISKKG++FKL+T+++++  EK Q G HS  ED K IR IY  IENQ  D++   +KL +KKYS  EY
Sbjct:    1 MGISKKGQWFKLQTLVEEICGEKTQTGFHSAKEDAKSIRLIYKTIENQWEDHIKCPQKLISKKYSFAEY 69
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BLAST of SMED30034100 vs. Planmine SMEST
Match: SMESG000049843.1 (SMESG000049843.1)

HSP 1 Score: 82.0333 bits (201), Expect = 1.067e-17
Identity = 38/78 (48.72%), Postives = 55/78 (70.51%), Query Frame = 3 
Query:   30 ATAHALQIIGISKKGEYFKLKTVIQDMFNEKMQFGIHSTLEDVKCIRRIYLKIENQRVDYVNLAKKLPAKKYSLEEYR 263
            A A   +  GI++ GE++KLKT++Q +  E+MQ GIHS LE+VK IR++YLK+E+Q +D V      P +KYSL EY+
Sbjct:  757 ADAQLFKSFGITRNGEWYKLKTLVQKICGEEMQQGIHSALENVKGIRKVYLKVEHQWIDDVEWKTINPPRKYSLSEYK 834
[Close]
BLAST of SMED30034100 vs. Planmine SMEST
Match: SMESG000052631.1 (SMESG000052631.1)

HSP 1 Score: 75.485 bits (184), Expect = 1.717e-15
Identity = 40/80 (50.00%), Postives = 52/80 (65.00%), Query Frame = 3 
Query:   21 RPTATAHALQIIGISKKGEYFKLKTVIQDMFNEKMQFGIHSTLEDVKCIRRIYLKIENQRVDYVNLAKKLPAKKYSLEEY 260
            R  A A   + +GISKKG++FKL+T+ +++  EK Q G HS   D K IRRIY  IENQ  D V   +K+ +KKYSL EY
Sbjct:  681 RDLAAALIFEKMGISKKGQWFKLQTLAEEICGEKTQTGSHSAKGDAKSIRRIYKTIENQWEDPVKWPQKVISKKYSLAEY 760
The following BLAST results are available for this feature:
BLAST of SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 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 SMED30034100 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000034928.16.361e-2245.56SMESG000034928.1[more]
SMESG000058166.11.031e-1875.56SMESG000058166.1[more]
SMESG000025296.11.016e-1752.17SMESG000025296.1[more]
SMESG000049843.11.067e-1748.72SMESG000049843.1[more]
SMESG000052631.11.717e-1550.00SMESG000052631.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034100 ID=SMED30034100|Name=SMED30034100|organism=Schmidtea mediterranea sexual|type=transcript|length=702bp
GGATGAGTTCTTTCTTGAAACGCCCAACAGCAACAGCACACGCTCTGCAG
ATCATTGGAATATCGAAAAAAGGTGAATACTTTAAGTTGAAAACGGTTAT
CCAGGATATGTTTAATGAAAAAATGCAGTTTGGGATCCATTCTACATTGG
AAGATGTGAAATGTATACGCAGAATATATTTAAAAATTGAAAATCAAAGG
GTGGACTATGTAAATTTAGCAAAGAAGCTACCTGCAAAGAAATATTCGTT
GGAAGAATATCGAAGATTCCATGAAAATGAAACAATTTCTGCAAACAACA
ACATCCAAAGGAACTATTGGTATTCTTAAAGAGAGCGAAACTCCAACTGA
TCAGTTAAAAAGTCTAACTGAACTGTATCTGGATCCAATAGAAAAAAATT
TGGTGGTAATAAGGAACCCAGTAATCCAGAGAATTCAGGTATCATTTGAG
TATGGGCCAATTCTCTATTTTGAAAAAAATCAGAAAAAGGAGACATTCAT
TCAGAATATGTGCCAGCGAAACCATCATGGTGTATGTTATTGTGTATCGA
CGAGAGAAAACATTCATTCGGTATGTAAGCGAAGCTGGCAAGATTGAATA
AAATATCGATTAAAAGTTATTGTTACTTATATCTAAAATTAAAATTTATT
AAAAATGTTTTTCGTCTTTTTTTTGTGATTTTCGGCGTCCCATTCCAAAA
AA
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protein sequence of SMED30034100-orf-1

>SMED30034100-orf-1 ID=SMED30034100-orf-1|Name=SMED30034100-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
MSSFLKRPTATAHALQIIGISKKGEYFKLKTVIQDMFNEKMQFGIHSTLE
DVKCIRRIYLKIENQRVDYVNLAKKLPAKKYSLEEYRRFHENETISANNN
IQRNYWYS*
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protein sequence of SMED30034100-orf-2

>SMED30034100-orf-2 ID=SMED30034100-orf-2|Name=SMED30034100-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
MKMKQFLQTTTSKGTIGILKESETPTDQLKSLTELYLDPIEKNLVVIRNP
VIQRIQVSFEYGPILYFEKNQKKETFIQNMCQRNHHGVCYCVSTRENIHS
VCKRSWQD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte