SMED30006384

Overview
NameSMED30006384
Smed IDSMED30006384
Length (bp)425
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30006384 (SMED30006384) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30006384 (SMED30006384) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30006384

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30006384 dd_Smed_v4_45827_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30006384 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000049:153485..153891 -1104
v31.000049:165785..166140 +1068
v31.000029:178972..179370 -1067
v31.001081:103625..103976 -1060
Homology
BLAST of SMED30006384 vs. Planmine SMEST
Match: SMESG000047477.1 (SMESG000047477.1)

HSP 1 Score: 113.235 bits (282), Expect = 3.063e-33
Identity = 62/107 (57.94%), Postives = 74/107 (69.16%), Query Frame = 3
Query:   33 MAHLEQAKKVVVNPVPAESINTNNISFPAENSHFVRAPVVQDSMALNIPVSVDQFNLNFPEKFKLAIAAGXXXXXXXEVIDLNELPGLEIPTSSPYANIVVRSCNKE 353
            MAHLEQAK+V+ NP P  S   + IS    NSH + APV  D MALNI V+VDQ NLNF EKFKLAIAAGQR+++  E+ID + LPGL   T+SPY N+V     KE
Sbjct:    1 MAHLEQAKEVIGNPAPTTSTTESIISPVTGNSHHINAPVAPDDMALNIRVTVDQLNLNFLEKFKLAIAAGQRKKRVPEIIDPSSLPGLSALTASPYTNLVTGRATKE 107          
BLAST of SMED30006384 vs. Planmine SMEST
Match: SMESG000028853.1 (SMESG000028853.1)

HSP 1 Score: 111.694 bits (278), Expect = 5.398e-31
Identity = 61/117 (52.14%), Postives = 79/117 (67.52%), Query Frame = 3
Query:    3 ERRRADHALLMAHLEQAKKVVVNPVPAESINTNNISFPAENSHFVRAPVVQDSMALNIPVSVDQFNLNFPEKFKLAIAAGXXXXXXXEVIDLNELPGLEIPTSSPYANIVVRSCNKE 353
            E+R+A+ ALL+A LEQAK+++ NP P+ S   NN S   EN H V A   +D MAL I V+VDQ N+NF +KFK AIAAG   Q++ E+IDL+ LPGL  P SSPY N++     KE
Sbjct:  120 EQRQAEQALLIAQLEQAKEIISNPAPSTSAIENNRSPGMENLHLVNALATRDDMALIIRVTVDQLNVNFSDKFKFAIAAG---QRKSEIIDLSGLPGLITPASSPYTNVLTGRTTKE 233          
BLAST of SMED30006384 vs. Planmine SMEST
Match: SMESG000054550.1 (SMESG000054550.1)

HSP 1 Score: 79.7221 bits (195), Expect = 1.221e-19
Identity = 53/124 (42.74%), Postives = 72/124 (58.06%), Query Frame = 3
Query:   33 MAHLEQAKKVVVNPVPAES-INTNNISFPAENSHFVRAPVVQDSMALNIPVSVDQFNLNFPEKFKLAIAAGXXXXXXXEVIDLNELPGLEIPTSSPYANIVVRSCNKERHGQSTNVLETSMFPC 401
            +AHLE+A   V  P+P+ S I  + +S   E+  F   P   D MALNI +++DQ N+NFPE+FKLAIA GQ RQ++ EVIDL ELPGL I  +  Y+ +   S  K+   Q     +    P 
Sbjct:   27 LAHLEKANVNVPAPIPSISPIEHHQVSR-EEDPCFATMPA-HDDMALNIRLTMDQLNVNFPERFKLAIATGQWRQKKLEVIDLRELPGLTIALARSYSKVATESILKKGMEQPRQTSKRRYLPV 148          
BLAST of SMED30006384 vs. Planmine SMEST
Match: SMESG000059356.1 (SMESG000059356.1)

HSP 1 Score: 63.1586 bits (152), Expect = 8.346e-14
Identity = 37/86 (43.02%), Postives = 50/86 (58.14%), Query Frame = 3
Query:  144 PVVQDSMALNIPVSVDQFNLNFPEKFKLAIAAGXXXXXXXEVIDLNELPGLEIPTSSPYANIVVRSCNKERHGQSTNVLETSMFPC 401
            P   D M LNI +++DQ N+NFPE+FKL IA GQRRQ++ EVIDL+EL  L IP+   Y  +  +   K    +     +   FP 
Sbjct:    2 PADHDDMVLNIRLTMDQSNVNFPERFKLVIAEGQRRQKKPEVIDLSELLELTIPSVRSYTKLATKRIVKSGMDKLRQTPKRRYFPV 87          
BLAST of SMED30006384 vs. Planmine SMEST
Match: SMESG000019166.1 (SMESG000019166.1)

HSP 1 Score: 57.3806 bits (137), Expect = 6.365e-12
Identity = 30/47 (63.83%), Postives = 36/47 (76.60%), Query Frame = -2
Query:  155 SPGSSLRSITSCLCCRR*PAAMANLNFSGKFRLNWSTDTGIFRAILS 295
            +PG+ LRSITS + C R PAAM NLNFSGKF+ +WST   +FRAI S
Sbjct:    3 NPGNPLRSITSGMRCLRCPAAMTNLNFSGKFKFSWSTVNRMFRAISS 49          
The following BLAST results are available for this feature:
BLAST of SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 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 SMED30006384 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000047477.13.063e-3357.94SMESG000047477.1[more]
SMESG000028853.15.398e-3152.14SMESG000028853.1[more]
SMESG000054550.11.221e-1942.74SMESG000054550.1[more]
SMESG000059356.18.346e-1443.02SMESG000059356.1[more]
SMESG000019166.16.365e-1263.83SMESG000019166.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006384 ID=SMED30006384|Name=SMED30006384|organism=Schmidtea mediterranea sexual|type=transcript|length=425bp
TCGAACGACGGCGGGCTGACCACGCTCTATTAATGGCTCATCTGGAACAG
GCGAAAAAAGTAGTCGTGAACCCCGTTCCAGCAGAATCCATCAACACAAA
TAATATTTCATTCCCAGCGGAAAATTCTCACTTCGTAAGGGCACCTGTTG
TTCAAGATAGTATGGCCCTGAATATTCCAGTGTCGGTCGACCAGTTCAAT
CTGAATTTCCCGGAGAAATTCAAGTTAGCCATAGCTGCCGGTCAGCGGCG
ACAGCAGAGACAAGAGGTTATTGACCTCAACGAACTTCCCGGACTAGAAA
TTCCAACCTCTAGTCCTTATGCAAATATAGTGGTCCGGTCGTGCAATAAA
GAGAGACACGGACAAAGTACGAACGTACTTGAGACGTCGATGTTTCCCTG
TAGATATCGACGAGTTAAAACCAAC
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protein sequence of SMED30006384-orf-1

>SMED30006384-orf-1 ID=SMED30006384-orf-1|Name=SMED30006384-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp
ERRRADHALLMAHLEQAKKVVVNPVPAESINTNNISFPAENSHFVRAPVV
QDSMALNIPVSVDQFNLNFPEKFKLAIAAGQRRQQRQEVIDLNELPGLEI
PTSSPYANIVVRSCNKERHGQSTNVLETSMFPCRYRRVKTN
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