SMED30008330

Overview
NameSMED30008330
Smed IDSMED30008330
Length (bp)720
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 SMED30008330 (SMED30008330) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008330 (SMED30008330) 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 SMED30008330 (SMED30008330) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008330 (SMED30008330) 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



SMED30008330

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
X1 cellSMED30008330SMESG000065342.1 SmedASXL_008944SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30008330 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014661:7898..8666 +3527
Homology
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BLAST of SMED30008330 vs. TrEMBL
Match: A0A5K3F8W5 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 1.981e-6
Identity = 39/135 (28.89%), Postives = 76/135 (56.30%), Query Frame = 2 
Query:  266 TRKVIDFSSKIDVGVRVLSLKLSRAQQVSGLI-KTKSNNVLYEVIGQI-ENVDYQSENEMVTFYIRD----GHCVQ-KSVFCNIDQIEFDINLNVVYRFVGFFNLALKSCFQCFKLIPINDEEFRIIKLFEVQSE 649
            T+K ++ SS    G+RV S+ + R + ++ ++ K ++   ++E +G I E+ +  S +  V FY+ +       VQ K  F +ID I  +I    +YR VG F+  +K  FQC+ + P +D+E ++ ++ ++ S+
Sbjct:   51 TQKTLEMSS---AGLRVFSVPVRRIRGLTPMLNKLENCPYIFETVGTIVESDETPSLSHSVAFYLEELANKSRGVQLKCNFSDIDGIHPEIYYGRIYRCVGKFS-TIKGTFQCYSITPCDDDELKLQEILQMHSD 181
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BLAST of SMED30008330 vs. TrEMBL
Match: A0A0R3ULN1 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS8593 PE=4 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 2.676e-6
Identity = 39/138 (28.26%), Postives = 77/138 (55.80%), Query Frame = 2 
Query:  266 TRKVIDFSSKIDVGVRVLSLKLSRAQQVSGLI-KTKSNNVLYEVIGQI-ENVDYQSENEMVTFYIRD----GHCVQ-KSVFCNIDQIEFDINLNVVYRFVGFFNLALKSCFQCFKLIPINDEEFRIIKLFEVQSEKQL 658
            T+K ++ SS    G+RV S+ + R + ++ ++ K ++   ++E +G I E+ +  S +  V FY+ +       VQ K  F +ID I  +I    +YR VG F+  +K  FQC+ + P +D+E ++ ++ ++ S+  +
Sbjct:   86 TQKTLEMSS---AGLRVFSVPVRRIRGLTPMLNKLENCPYIFETVGTIVESDETPSLSHSVAFYLEELANKSRGVQLKCNFSDIDGIHPEIYYGRIYRCVGKFS-TIKGTFQCYSITPCDDDELKLQEILQMHSDNAI 219
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BLAST of SMED30008330 vs. Planmine SMEST
Match: SMESG000065342.1 (SMESG000065342.1)

HSP 1 Score: 402.519 bits (1033), Expect = 1.562e-144
Identity = 200/203 (98.52%), Postives = 201/203 (99.01%), Query Frame = 2 
Query:   59 MSYYKNEKPKYNLDYNFNANVGRSSRRDELQGDCNDKYVNSKNLNSIQPLDKSVNKLTKIVSSDKTRNQTRKVIDFSSKIDVGVRVLSLKLSRAQQVSGLIKTKSNNVLYEVIGQIENVDYQSENEMVTFYIRDGHCVQKSVFCNIDQIEFDINLNVVYRFVGFFNLALKSCFQCFKLIPINDEEFRIIKLFEVQSEKQLQLM 667
            MSYYKNEKPKYNLDYNFNANVGRSSRRDELQGDCNDKYVNSK LNSIQPLDK+VNKLTKIVSSDKTRNQTRKVIDFSSKIDVGVRVLSLKLSRAQQVS LIKTKSNNVLYEVIGQIENVDYQSENEMVTFYIRDGHCVQKSVFCNIDQIEFDINLNVVYRFVGFFNLALKSCFQCFKLIPINDEEFRIIKLFEVQSEKQLQLM
Sbjct:    1 MSYYKNEKPKYNLDYNFNANVGRSSRRDELQGDCNDKYVNSKTLNSIQPLDKNVNKLTKIVSSDKTRNQTRKVIDFSSKIDVGVRVLSLKLSRAQQVSSLIKTKSNNVLYEVIGQIENVDYQSENEMVTFYIRDGHCVQKSVFCNIDQIEFDINLNVVYRFVGFFNLALKSCFQCFKLIPINDEEFRIIKLFEVQSEKQLQLM 203
The following BLAST results are available for this feature:
BLAST of SMED30008330 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 SMED30008330 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 SMED30008330 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 SMED30008330 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 SMED30008330 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 SMED30008330 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 SMED30008330 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 SMED30008330 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A5K3F8W51.981e-628.89Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A0R3ULN12.676e-628.26Uncharacterized protein OS=Mesocestoides corti OX=... [more]
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BLAST of SMED30008330 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 SMED30008330 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 SMED30008330 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 SMED30008330 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 SMED30008330 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 SMED30008330 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000065342.11.562e-14498.52SMESG000065342.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008330 ID=SMED30008330|Name=SMED30008330|organism=Schmidtea mediterranea sexual|type=transcript|length=720bp
CAACATTTTGATTTTTAGGAAGGAATTTTAAAATATAATTAAGCATTTGA
GGTAACAAATGAGTTATTATAAAAACGAGAAACCTAAATATAATTTGGAT
TATAATTTTAATGCAAATGTTGGTAGGAGTTCCCGAAGAGATGAGTTGCA
AGGTGATTGTAATGATAAATATGTTAATTCTAAAAACCTTAATTCAATTC
AACCGTTGGACAAAAGTGTAAATAAATTAACTAAAATTGTTTCCAGCGAT
AAGACTCGAAATCAAACGAGAAAAGTTATTGACTTCAGTAGCAAAATTGA
TGTTGGTGTTAGAGTTTTAAGCTTGAAATTGAGTCGGGCTCAACAGGTGT
CAGGTTTAATAAAAACCAAATCTAATAATGTACTATACGAAGTAATTGGT
CAGATTGAAAATGTTGATTACCAATCGGAAAATGAAATGGTCACATTTTA
TATTCGCGATGGACATTGTGTCCAGAAATCCGTTTTCTGTAACATTGACC
AAATAGAATTCGACATAAATTTGAATGTAGTCTACCGATTTGTTGGATTT
TTCAATTTAGCTCTCAAATCATGTTTCCAGTGTTTCAAACTCATCCCAAT
CAACGATGAAGAATTTAGAATCATCAAATTGTTCGAGGTGCAATCTGAAA
AGCAACTGCAGTTAATGCTGTCAAATATTTCTGAGATTTAATCGATTTTG
TTGTTTGTTTTAATTTTGTG
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protein sequence of SMED30008330-orf-1

>SMED30008330-orf-1 ID=SMED30008330-orf-1|Name=SMED30008330-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=211bp
MSYYKNEKPKYNLDYNFNANVGRSSRRDELQGDCNDKYVNSKNLNSIQPL
DKSVNKLTKIVSSDKTRNQTRKVIDFSSKIDVGVRVLSLKLSRAQQVSGL
IKTKSNNVLYEVIGQIENVDYQSENEMVTFYIRDGHCVQKSVFCNIDQIE
FDINLNVVYRFVGFFNLALKSCFQCFKLIPINDEEFRIIKLFEVQSEKQL
QLMLSNISEI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell