SMED30028980

Overview
NameSMED30028980
Smed IDSMED30028980
Length (bp)780
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 SMED30028980 (SMED30028980) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028980 (SMED30028980) 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 SMED30028980 (SMED30028980) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028980 (SMED30028980) 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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Homology
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BLAST of SMED30028980 vs. TrEMBL
Match: A0A1I8HA02 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 3.888e-10
Identity = 33/81 (40.74%), Postives = 48/81 (59.26%), Query Frame = 3 
Query:  309 QIDRDIHPYGETRCYSDIIFGQREVKVKLDHTKFLAWISFVVFLLIISATIIVLAVLYQENHTNLEKNVELAKSSADTPTF 551
            Q DRD+HPYG    +  +++ +R VKV++DH KFLAWI F  F+L+ S  II+LA +  E      ++ +L  S   TP  
Sbjct:   58 QEDRDLHPYGRGGRFEGVLYSRR-VKVQVDHAKFLAWIVFAGFILLTSGAIIILAEM--ERRQKTLQHQQLLASVTQTPAL 135
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BLAST of SMED30028980 vs. TrEMBL
Match: A0A1I8IHX0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 4.964e-9
Identity = 29/63 (46.03%), Postives = 42/63 (66.67%), Query Frame = 3 
Query:  309 QIDRDIHPYGETRCYSDIIFGQREVKVKLDHTKFLAWISFVVFLLIISATIIVLAVLYQENHT 497
            Q DRD+HPYG    +  +++ +R VKV++DH KFLAWI F  F+L+ S  II+LA + +   T
Sbjct:   58 QEDRDLHPYGRGGRFEGVLYSRR-VKVQVDHAKFLAWIVFAGFILLTSGAIIILAEMERRQKT 119
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BLAST of SMED30028980 vs. Planmine SMEST
Match: SMESG000047330.1 (SMESG000047330.1)

HSP 1 Score: 166.777 bits (421), Expect = 2.399e-52
Identity = 96/99 (96.97%), Postives = 97/99 (97.98%), Query Frame = 3 
Query:  177 MSCEFSQNQPLLNPLLIDSILHTYXXXXXXXXXXXXXXDQNYILQIDRDIHPYGETRCYSDIIFGQREVKVKLDHTKFLAWISFVVFLLIISATIIVLA 473
            MSCEFSQNQPLLNPLL DS+LHTYSNESSSVSNSIRSRDQ YILQIDRDIHPYGETRCYSDIIFGQREVKVKLDHTKFLAWISFVVFLLIISATIIVLA
Sbjct:    1 MSCEFSQNQPLLNPLLNDSLLHTYSNESSSVSNSIRSRDQTYILQIDRDIHPYGETRCYSDIIFGQREVKVKLDHTKFLAWISFVVFLLIISATIIVLA 99
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BLAST of SMED30028980 vs. Planmine SMEST
Match: SMESG000061686.1 (SMESG000061686.1)

HSP 1 Score: 151.754 bits (382), Expect = 2.792e-45
Identity = 77/90 (85.56%), Postives = 80/90 (88.89%), Query Frame = 1 
Query:  511 MSNLPNLPRIPQLSPSAIATRQKLDQLERDHAILQAKY*KINGTWSSPDATRSLYQNISRLSRTRDDLIIETRSQRITIVEQSAALRRIF 780
            MSNL NLPRIP+LS SAIATRQKLDQLERDHAILQAKY  I GTWSSP+A RSLYQ +SRLSR RDDLIIETRSQRITI EQSAALR IF
Sbjct:    1 MSNLSNLPRIPRLSSSAIATRQKLDQLERDHAILQAKYRNIKGTWSSPEAARSLYQKVSRLSRARDDLIIETRSQRITIAEQSAALRPIF 90
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BLAST of SMED30028980 vs. Planmine SMEST
Match: SMESG000046818.1 (SMESG000046818.1)

HSP 1 Score: 153.68 bits (387), Expect = 1.298e-42
Identity = 78/91 (85.71%), Postives = 82/91 (90.11%), Query Frame = 1 
Query:  508 KMSNLPNLPRIPQLSPSAIATRQKLDQLERDHAILQAKY*KINGTWSSPDATRSLYQNISRLSRTRDDLIIETRSQRITIVEQSAALRRIF 780
            +MSNL NLPRIP+LS S IATRQKLDQLERDHA+LQAKY KI GTWSSP+ATRSLYQ ISRL R RDDLIIETRSQRITI EQSAALRRIF
Sbjct:  137 EMSNLSNLPRIPRLSSSTIATRQKLDQLERDHALLQAKYEKIKGTWSSPEATRSLYQKISRLFRARDDLIIETRSQRITIAEQSAALRRIF 227
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BLAST of SMED30028980 vs. Planmine SMEST
Match: SMESG000068149.1 (SMESG000068149.1)

HSP 1 Score: 142.124 bits (357), Expect = 1.804e-39
Identity = 75/108 (69.44%), Postives = 86/108 (79.63%), Query Frame = 1 
Query:  457 PSLFLQFYTKRTIPISRKMSNLPNLPRIPQLSPSAIATRQKLDQLERDHAILQAKY*KINGTWSSPDATRSLYQNISRLSRTRDDLIIETRSQRITIVEQSAALRRIF 780
            P L+L    +  +P S +MSNL NLP+ P+LS S +ATRQKLDQLERDHAIL+AKY K+ GTWSSP+ T +LYQ ISRLSR RDDLIIETR QRITI EQSAAL RIF
Sbjct:    5 PHLYLAL-NRENLPTS-EMSNLSNLPQKPRLSSSTVATRQKLDQLERDHAILRAKYEKLKGTWSSPETTSNLYQRISRLSRARDDLIIETRGQRITIAEQSAALTRIF 110
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BLAST of SMED30028980 vs. Planmine SMEST
Match: SMESG000071773.1 (SMESG000071773.1)

HSP 1 Score: 130.568 bits (327), Expect = 2.347e-37
Identity = 62/85 (72.94%), Postives = 75/85 (88.24%), Query Frame = 1 
Query:  526 NLPRIPQLSPSAIATRQKLDQLERDHAILQAKY*KINGTWSSPDATRSLYQNISRLSRTRDDLIIETRSQRITIVEQSAALRRIF 780
            +LPRIP+LSPS IATRQKL+QL++DH +LQAKY K+ GTWSSP+ATR L+Q  SRLSR RDDL++E+RSQRI I +QSAALRRIF
Sbjct:    3 DLPRIPRLSPSIIATRQKLEQLQKDHTVLQAKYQKLKGTWSSPEATRKLFQKSSRLSRARDDLVVESRSQRILIAKQSAALRRIF 87
The following BLAST results are available for this feature:
BLAST of SMED30028980 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 SMED30028980 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 SMED30028980 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 SMED30028980 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 SMED30028980 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 SMED30028980 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 SMED30028980 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 SMED30028980 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A1I8HA023.888e-1040.74Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8IHX04.964e-946.03Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30028980 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 SMED30028980 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 SMED30028980 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 SMED30028980 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 SMED30028980 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 SMED30028980 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000047330.12.399e-5296.97SMESG000047330.1[more]
SMESG000061686.12.792e-4585.56SMESG000061686.1[more]
SMESG000046818.11.298e-4285.71SMESG000046818.1[more]
SMESG000068149.11.804e-3969.44SMESG000068149.1[more]
SMESG000071773.12.347e-3772.94SMESG000071773.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028980 ID=SMED30028980|Name=SMED30028980|organism=Schmidtea mediterranea sexual|type=transcript|length=780bp
TATGCGTCATTGTTATTACCTACTCTAGTTGGAGAAGAAAATTAAATTAT
TTTGATTAAATGAATGGATACGATTTGATTTGAGAATAGTATTTCTATGT
ATTTATTTCATCTCACATTTATAAATTCTTTAATTTAAAATGTTTTTGAA
AATGAAATAAAAGTGATATCATCTCAATGTCTTGTGAATTTTCTCAAAAC
CAACCATTATTGAACCCGCTGCTCATTGATTCGATATTGCATACATACTC
AAATGAATCTTCTAGTGTTTCAAATAGCATTCGAAGCAGAGATCAAAATT
ATATTTTACAAATAGATAGGGATATTCATCCCTATGGAGAGACTCGGTGC
TATAGTGATATTATATTTGGACAAAGAGAAGTAAAAGTTAAACTGGATCA
TACGAAATTCTTAGCATGGATATCATTTGTGGTCTTTCTTTTAATTATAT
CAGCCACCATCATTGTTCTTGCAGTTCTATACCAAGAGAACCATACCAAT
CTCGAGAAAAATGTCGAACTTGCCAAATCTTCCGCGGATACCCCAACTTT
CCCCATCTGCGATAGCCACTAGACAGAAACTTGATCAACTAGAGAGAGAT
CACGCCATTCTACAGGCGAAATATTAGAAAATAAACGGCACATGGAGTTC
GCCCGATGCAACCCGCAGTTTGTATCAAAATATCTCTCGCCTTTCTCGGA
CCAGAGATGACCTTATAATCGAAACTCGAAGTCAGCGAATCACGATCGTT
GAACAAAGTGCCGCGCTTCGACGGATATTT
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protein sequence of SMED30028980-orf-1

>SMED30028980-orf-1 ID=SMED30028980-orf-1|Name=SMED30028980-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=132bp
MSCEFSQNQPLLNPLLIDSILHTYSNESSSVSNSIRSRDQNYILQIDRDI
HPYGETRCYSDIIFGQREVKVKLDHTKFLAWISFVVFLLIISATIIVLAV
LYQENHTNLEKNVELAKSSADTPTFPICDSH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000418head
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 80..102