SMED30007174

Overview
NameSMED30007174
Smed IDSMED30007174
Length (bp)711
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 SMED30007174 (SMED30007174) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007174 (SMED30007174) 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 SMED30007174 (SMED30007174) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007174 (SMED30007174) 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



SMED30007174

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30007174h1SMcG0003059 SmedASXL_006605SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30007174h1SMcG0003059 dd_Smed_v4_3155_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30007174h1SMcG0003059 dd_Smed_v4_3155_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30007174h1SMcG0003059 dd_Smed_v4_3155_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007174h1SMcG0003059 dd_Smed_v4_3155_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
SMED30007174 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001695:139905..140618 +3526
Homology
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BLAST of SMED30007174 vs. Planmine SMEST
Match: SMESG000027686.1 (SMESG000027686.1)

HSP 1 Score: 172.555 bits (436), Expect = 2.152e-52
Identity = 81/81 (100.00%), Postives = 81/81 (100.00%), Query Frame = 1 
Query:  412 GCVWRESHYPKFKQPACCKQRLKYKISPFSLWVQKNMKSLKGKGDASQIMRALAKSWKCLSPMDKAKFYQKAAGSKKQKCD 654
            GCVWRESHYPKFKQPACCKQRLKYKISPFSLWVQKNMKSLKGKGDASQIMRALAKSWKCLSPMDKAKFYQKAAGSKKQKCD
Sbjct:  238 GCVWRESHYPKFKQPACCKQRLKYKISPFSLWVQKNMKSLKGKGDASQIMRALAKSWKCLSPMDKAKFYQKAAGSKKQKCD 318
[Close]
BLAST of SMED30007174 vs. Planmine SMEST
Match: SMESG000040544.1 (SMESG000040544.1)

HSP 1 Score: 77.411 bits (189), Expect = 2.428e-18
Identity = 36/36 (100.00%), Postives = 36/36 (100.00%), Query Frame = 1 
Query:   55 MSNLTSNVNNYVPSVFDSNAQGIIPSIFNDINNSAC 162
            MSNLTSNVNNYVPSVFDSNAQGIIPSIFNDINNSAC
Sbjct:    1 MSNLTSNVNNYVPSVFDSNAQGIIPSIFNDINNSAC 36
The following BLAST results are available for this feature:
BLAST of SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 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 SMED30007174 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000027686.12.152e-52100.00SMESG000027686.1[more]
SMESG000040544.12.428e-18100.00SMESG000040544.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007174 ID=SMED30007174|Name=SMED30007174|organism=Schmidtea mediterranea sexual|type=transcript|length=711bp
TAAAAATCAATTATTTTAAATTTTTAAATGCTTAGTTATATTTGATTTTT
CTAAATGTCTAATTTAACATCCAATGTTAACAATTACGTGCCTTCGGTTT
TCGATTCTAATGCACAAGGAATTATTCCATCTATATTTAATGACATAAAT
AATAGTGCATGTCGAAAGAGAAGTCGATCTAAAAGACGTCATCATCGTAA
ACGGAGGAGAGCAAGTAGAAGCAAATCTAGAAAAAGAAAACGAAGGAGAG
CTAGAAGGAGAAGACGGTCAAGAAGAAAAAGTAGGTCAAAAGTTAAAAGT
AGATCAAGAAGTGGATCTAGGAAAAGAAGACGAATGACTGGATCTAGATG
TCGAGTCAAGACTCGAAAAAGAAAATCTCGTGTGTCTACTAGTAAATGTA
GCAAACGTAAAGGTTGTGTATGGAGGGAAAGTCATTATCCTAAGTTTAAA
CAGCCTGCCTGTTGTAAACAAAGATTAAAATATAAAATATCACCGTTTTC
TCTATGGGTACAAAAAAATATGAAAAGCTTAAAAGGGAAAGGTGACGCTT
CTCAAATTATGAGAGCTTTGGCTAAAAGTTGGAAATGTTTAAGTCCAATG
GATAAAGCTAAATTTTACCAGAAAGCAGCTGGTTCTAAAAAGCAAAAATG
CGACTAATACGTTACAGTATATTTTATTTAATTAAAATACATTTTTTTTC
AAATAAAAAAA
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protein sequence of SMED30007174-orf-1

>SMED30007174-orf-1 ID=SMED30007174-orf-1|Name=SMED30007174-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=201bp
MSNLTSNVNNYVPSVFDSNAQGIIPSIFNDINNSACRKRSRSKRRHHRKR
RRASRSKSRKRKRRRARRRRRSRRKSRSKVKSRSRSGSRKRRRMTGSRCR
VKTRKRKSRVSTSKCSKRKGCVWRESHYPKFKQPACCKQRLKYKISPFSL
WVQKNMKSLKGKGDASQIMRALAKSWKCLSPMDKAKFYQKAAGSKKQKCD
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR036910HMG_box_dom_sf
IPR009071HMG_box_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036910High mobility group box domain superfamilyGENE3DG3DSA:1.10.30.10coord: 129..199
e-value: 3.3E-7
score: 32.4
IPR036910High mobility group box domain superfamilySUPERFAMILYSSF47095HMG-boxcoord: 140..196
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 38..112
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 34..112
NoneNo IPR availableCDDcd00084HMG-boxcoord: 145..197
e-value: 8.90362E-6
score: 39.9096
IPR009071High mobility group box domainPROSITEPS50118HMG_BOX_2coord: 141..200
score: 9.047