SMED30028552

Overview
NameSMED30028552
Smed IDSMED30028552
Length (bp)438
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30028552 (SMED30028552) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028552 (SMED30028552) 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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Anatomical Expression

PAGE et. al., 2020




SMED30028552

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30028552SMESG000035333.1 SMESG000035329.1 SmedASXL_016645SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
tail regionSMED30028552SMESG000035333.1 SMESG000035330.1 SMESG000035329.1 SMESG000035328.1 SMESG000035326.1 SmedASXL_074705SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
gutSMED30028552SMESG000035329.1 SMESG000035328.1 SMESG000035326.1 dd_Smed_v4_19_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30028552SMESG000035333.1 SMESG000035330.1 SMESG000035329.1 SMESG000035328.1 SMESG000035326.1 Contig51562newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30028552SMESG000035333.1 SMESG000035330.1 SMESG000035329.1 SMESG000035328.1 SMESG000035326.1 Contig51562uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30028552SMESG000035333.1 SMESG000035330.1 SMESG000035329.1 SMESG000035328.1 SMESG000035326.1 Contig16655newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30028552SMESG000035333.1 SMESG000035330.1 SMESG000035329.1 SMESG000035328.1 SMESG000035326.1 Contig16655uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
body wall musculatureSMED30028552SMESG000035329.1 SMESG000035328.1 SMESG000035326.1 dd_Smed_v4_19_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30028552SMESG000035330.1 SMED_05187_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028552 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.016296:6637..7636 -1899
v31.013637:4666..5665 -1893
v31.015535:9300..10303 +1889
v31.019806:1698..2642 +1793
v31.016442:4614..8799 -1572
v31.016442:4237..8422 +1043
Homology
BLAST of SMED30028552 vs. Planmine SMEST
Match: SMESG000035326.1 (SMESG000035326.1)

HSP 1 Score: 225.328 bits (573), Expect = 3.429e-77
Identity = 108/118 (91.53%), Postives = 111/118 (94.07%), Query Frame = 2
Query:    2 MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDERYERGFEPFGRASQTRW 355
            MVSCT   TQTYGA EGFPTISRRQVQL K LLEN+A+KVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSR+ MGNVDERYERGFEPFGRASQTRW
Sbjct:   13 MVSCTRYETQTYGAPEGFPTISRRQVQLLKGLLENVASKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRHLMGNVDERYERGFEPFGRASQTRW 130          
BLAST of SMED30028552 vs. Planmine SMEST
Match: SMESG000035326.1 (SMESG000035326.1)

HSP 1 Score: 224.557 bits (571), Expect = 4.514e-77
Identity = 108/118 (91.53%), Postives = 111/118 (94.07%), Query Frame = 2
Query:    2 MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDERYERGFEPFGRASQTRW 355
            MVSCT   TQTYGA EGFPTISRRQVQL K LLEN+A+KVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSR+ MGNVDERYERGFEPFGRASQTRW
Sbjct:    1 MVSCTRYETQTYGAPEGFPTISRRQVQLLKGLLENVASKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRHLMGNVDERYERGFEPFGRASQTRW 118          
BLAST of SMED30028552 vs. Planmine SMEST
Match: SMESG000035330.1 (SMESG000035330.1)

HSP 1 Score: 219.164 bits (557), Expect = 7.566e-75
Identity = 106/110 (96.36%), Postives = 108/110 (98.18%), Query Frame = 2
Query:    2 MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDERYERGFEPF 331
            MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDE YER F+P+
Sbjct:    9 MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDESYERRFKPY 118          
BLAST of SMED30028552 vs. Planmine SMEST
Match: SMESG000035330.1 (SMESG000035330.1)

HSP 1 Score: 219.164 bits (557), Expect = 8.347e-75
Identity = 106/110 (96.36%), Postives = 108/110 (98.18%), Query Frame = 2
Query:    2 MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDERYERGFEPF 331
            MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDE YER F+P+
Sbjct:   13 MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDESYERRFKPY 122          
BLAST of SMED30028552 vs. Planmine SMEST
Match: SMESG000035333.1 (SMESG000035333.1)

HSP 1 Score: 219.164 bits (557), Expect = 1.266e-74
Identity = 105/117 (89.74%), Postives = 111/117 (94.87%), Query Frame = 2
Query:    2 MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMYLRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDERYERGFEPFGRASQTR 352
            MVSC  + TQTYGASEGFPTISRRQVQLFKNLLENIA+KVTEEPENLSMYLRSFKVK IVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDERYE+GF+PFGR ++ R
Sbjct:   13 MVSCIRLETQTYGASEGFPTISRRQVQLFKNLLENIASKVTEEPENLSMYLRSFKVKKIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVDERYEQGFQPFGRVNKLR 129          
The following BLAST results are available for this feature:
BLAST of SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 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 SMED30028552 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000035326.13.429e-7791.53SMESG000035326.1[more]
SMESG000035326.14.514e-7791.53SMESG000035326.1[more]
SMESG000035330.17.566e-7596.36SMESG000035330.1[more]
SMESG000035330.18.347e-7596.36SMESG000035330.1[more]
SMESG000035333.11.266e-7489.74SMESG000035333.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028552 ID=SMED30028552|Name=SMED30028552|organism=Schmidtea mediterranea sexual|type=transcript|length=438bp
AATGGTTTCGTGCACTTATATTCCAACGCAAACATATGGTGCATCAGAGG
GGTTTCCTACGATAAGTCGAAGACAAGTGCAATTGTTTAAAAATTTACTA
GAAAATATCGCTGCGAAAGTCACAGAAGAACCGGAAAATCTTTCAATGTA
TTTAAGAAGCTTTAAAGTGAAGAATATTGTGAACCAATTGAACAGCCCGA
TTAGAAACAAAGTCAAAAAAATAATCAAACAATTAAAAGAAATAGTTGAA
GTAATAAAAGGTTTCCCAATGCATTCTCGCTACTTTATGGGAAATGTTGA
TGAAAGGTATGAAAGAGGCTTCGAACCATTCGGACGAGCTTCACAAACCC
GATGGTGATACACGAAATATTAATTAGTCGCCGAAGGATTAAACAATTAA
CATTAATTTGTTTATAATAAATAAATTTTCGCAGTTTT
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protein sequence of SMED30028552-orf-1

>SMED30028552-orf-1 ID=SMED30028552-orf-1|Name=SMED30028552-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=119bp
MVSCTYIPTQTYGASEGFPTISRRQVQLFKNLLENIAAKVTEEPENLSMY
LRSFKVKNIVNQLNSPIRNKVKKIIKQLKEIVEVIKGFPMHSRYFMGNVD
ERYERGFEPFGRASQTRW*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000240body wall musculature
PLANA:0000421tail
PLANA:0000429neoblast