SMED30002730

Overview
NameSMED30002730
Smed IDSMED30002730
Length (bp)1724
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 SMED30002730 (SMED30002730) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002730 (SMED30002730) 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 SMED30002730 (SMED30002730) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002730 (SMED30002730) 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



SMED30002730

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30002730SMESG000051170.1 dd_Smed_v4_10305_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002730SMESG000051170.1 dd_Smed_v4_10305_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30002730SMESG000051170.1 dd_Smed_v4_10305_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30002730SMESG000051170.1 dd_Smed_v4_8704_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002730SMESG000038294.1 Contig33398newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002730SMESG000038294.1 Contig33398uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30002730SMESG000051170.1 dd_Smed_v6_10305_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30002730SMESG000051170.1 dd_Smed_v6_8704_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002730 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006164:15089..17341 -7227
v31.001414:49513..52189 +7153
v31.001141:60478..61888 -6072
v31.002999:59909..63857 -5959
v31.004822:18383..19810 +5956
v31.002241:15035..16460 -5924
v31.002457:25988..27401 +5713
Homology
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BLAST of SMED30002730 vs. Planmine SMEST
Match: SMESG000047667.1 (SMESG000047667.1)

HSP 1 Score: 149.443 bits (376), Expect = 1.573e-37
Identity = 79/146 (54.11%), Postives = 99/146 (67.81%), Query Frame = 2 
Query: 1316 KKNKIMWGQTQTRWDEFDVTQMRS---HEGVHAE--------DHPAGGSSSQWSDVDRTTLTIPNRFVGMYRQALWDRGYYISTYDTPEWPNRNSDGRDADMELPSILIKNEPVRNPAREIRQVAEGALRRFELLERQYRYLANQQ 1720
            K+N  +  Q   R++E    +MR    H+ +H          +   G SSS+  DV+RTTLT+P++F G YRQALWDRGY ISTY TPEWPNRN D RD D++LPS++IK EP RNPAREIRQ +E AL + E LER+YR LANQQ
Sbjct: 1516 KRNNELLRQMGIRYEE--SKEMRINMIHKAIHGSRKTYDQHRNFNNGSSSSKCRDVERTTLTVPSKFAGRYRQALWDRGYSISTYGTPEWPNRNPDRRDEDIKLPSLVIKREPGRNPAREIRQESEEALYKLEQLERRYRRLANQQ 1659
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BLAST of SMED30002730 vs. Planmine SMEST
Match: SMESG000060519.1 (SMESG000060519.1)

HSP 1 Score: 146.747 bits (369), Expect = 8.530e-37
Identity = 70/100 (70.00%), Postives = 75/100 (75.00%), Query Frame = 2 
Query: 1424 GSSSQWSDVDRTTLTIPNRFVGMYRQALWDRGYYISTYDTPEWPNRNSDGRDADMELPSILIKNEPVRNPAREIRQVAEGALRRFELLERQYRYLANQQR 1723
             SSS+W DV+RTTLT+ NRF G Y QALWD GY ISTY T EWP RN + RD D ELP ILIK EP RNPAREIRQ AEGAL  FE L+R YR L NQQR
Sbjct:  850 ASSSKWVDVERTTLTVQNRFAGRYHQALWDPGYSISTYGTLEWPCRNPESRDKDTELPCILIKREPGRNPAREIRQKAEGALHHFEKLKRWYRPLTNQQR 949
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BLAST of SMED30002730 vs. Planmine SMEST
Match: SMESG000008335.1 (SMESG000008335.1)

HSP 1 Score: 144.05 bits (362), Expect = 3.629e-36
Identity = 66/96 (68.75%), Postives = 78/96 (81.25%), Query Frame = 2 
Query: 1436 QWSDVDRTTLTIPNRFVGMYRQALWDRGYYISTYDTPEWPNRNSDGRDADMELPSILIKNEPVRNPAREIRQVAEGALRRFELLERQYRYLANQQR 1723
            QW D++ TTLT+P+RF G YRQALWD+GY IST+ TPEWPNR S+  D D ELPS++IK EP RNPAREIRQ  EG L R+E LER+YRYLANQ+R
Sbjct:   92 QWRDMESTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKR 187
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BLAST of SMED30002730 vs. Planmine SMEST
Match: SMESG000054252.1 (SMESG000054252.1)

HSP 1 Score: 128.642 bits (322), Expect = 5.043e-34
Identity = 61/101 (60.40%), Postives = 71/101 (70.30%), Query Frame = 2 
Query: 1421 GGSSSQWSDVDRTTLTIPNRFVGMYRQALWDRGYYISTYDTPEWPNRNSDGRDADMELPSILIKNEPVRNPAREIRQVAEGALRRFELLERQYRYLANQQR 1723
            G  S  W DVD TTLT+P  F G Y QALW+ GY ISTY TP+WP R ++G + D ELPSILIK EP RNP REIRQ AEG L R E LE +YR+L  +Q+
Sbjct:   13 GTHSGNWKDVDLTTLTVPTLFAGRYTQALWNLGYTISTYGTPKWPYRKTNGPEGDFELPSILIKREPGRNPTREIRQKAEGELHRLEQLEWRYRFLVKRQK 113
[Close]
BLAST of SMED30002730 vs. Planmine SMEST
Match: SMESG000054252.1 (SMESG000054252.1)

HSP 1 Score: 129.798 bits (325), Expect = 6.109e-33
Identity = 61/101 (60.40%), Postives = 71/101 (70.30%), Query Frame = 2 
Query: 1421 GGSSSQWSDVDRTTLTIPNRFVGMYRQALWDRGYYISTYDTPEWPNRNSDGRDADMELPSILIKNEPVRNPAREIRQVAEGALRRFELLERQYRYLANQQR 1723
            G  S  W DVD TTLT+P  F G Y QALW+ GY ISTY TP+WP R ++G + D ELPSILIK EP RNP REIRQ AEG L R E LE +YR+L  +Q+
Sbjct:   13 GTHSGNWKDVDLTTLTVPTLFAGRYTQALWNLGYTISTYGTPKWPYRKTNGPEGDFELPSILIKREPGRNPTREIRQKAEGELHRLEQLEWRYRFLVKRQK 113
The following BLAST results are available for this feature:
BLAST of SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 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 SMED30002730 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000047667.11.573e-3754.11SMESG000047667.1[more]
SMESG000060519.18.530e-3770.00SMESG000060519.1[more]
SMESG000008335.13.629e-3668.75SMESG000008335.1[more]
SMESG000054252.15.043e-3460.40SMESG000054252.1[more]
SMESG000054252.16.109e-3360.40SMESG000054252.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002730 ID=SMED30002730|Name=SMED30002730|organism=Schmidtea mediterranea sexual|type=transcript|length=1724bp
AACAATTTGAGGTTAAAGGGAAGGGGTCTTGCGGAAATCGATGTAACGGA
CATGTCGAATTAAAATCCATTAACTATTTTATTAAAGCAGATAAGAGTTA
AATGATAATTCAATAAATAATAGAAGGTTTCAATAGAAATATTTTAAATG
ACTAAAGAAAAATGCTGTCGACAAGAGGTAAAAACTAGTCCGGTAAATAA
ATAAAGGTTAAAGTAAACTTATAAATTAAAACCCCAGCGATAACTAATTA
ATGAGTAAATTGGAAACTACCGAATAAAATAAGTAGTATCATATTATAGA
TAAAACGCAAAAAGGATTCCCAGAATTATTGTTAATAACTAAGCATCAGA
ACCCTACTATCGCCATACTTTAGATAAGCCGAATGTGTGATCAAAATTCC
AATTGATACCATCGCACTAAATAATAGTAAAGGTCAATCACCGAACCTAC
CAACATTAGATAATATCCCTTAAAGCCAACTTAAACCGCAATAATCATCC
TCATCTATTCTACAACTACCGAGAGTAGATACTTACAACAAGCTTCGACA
TAAAGTATTAACTCATCACCTCAATCGAAACTAAAAGGCAAGCCCAGATA
ATTTATTTATTAGTAAAAATCATCCCAAGATGTCCACCACTACCTCCGAA
CCATTATGAGTAGGCAACCATTGACAATCACTGAGACGTTCACTAACATC
GGAGCAGCAAATTTATTCCCCAGTTAAAGGACAACCGAACTGAGATAACG
GAAATTGAAATGCCACCTAACTGATATCGACGATGGCCAAACGAGAGGAT
ATACGAGGTAAATGCATCATGATTCGCTTGTAGTAGGCAAAGCAAATGCT
AAATTAAGTAAAGTTTAATCATTTTTCATAGCCATAATAGTTAAATAAAA
TCTCAACAAATAAAATTCCAAGAATTATGGTCGCAAAAATATAAAAATCA
ATTCGGAAGAAATTCCTTTTAACTCAAGAAAATACTGGACATGCCACGAA
CTAACACACATAATCAAGTAGAAGAAAATATGAAATATCGACTCATCAAG
ACCATATTTACTACAAGAAAATGCCGCCCTCAACAATCGACAGAAGGAAA
TTATAACAATGACCAATCGGCAGACGCCACCGCCAATTCAAGTTCTTACC
CGTCCGCGTGGAAGAAAAATCGATAGCTCATATAAATAGAGGCCCAGGTT
ACAACGAACGTCATCACTATTTCACTATTTCAACAGAAAACTTATGCCCA
AATTGACTGCAATGAATCAAGACAAATGCGATGTGGAAATGTTGGAGAAT
GTCAGAGCCTCCGCTAAGAAGAATAAGATAATGTGGGGACAAACACAAAC
CCGCTGGGATGAATTCGATGTCACCCAGATGCGTTCCCACGAGGGAGTCC
ATGCAGAAGATCACCCGGCAGGTGGATCAAGTAGTCAATGGAGTGATGTC
GATCGCACAACACTGACGATCCCAAACCGATTTGTAGGGATGTATCGCCA
GGCTCTATGGGATCGGGGGTATTACATATCGACCTATGATACTCCAGAAT
GGCCAAACCGGAATTCAGATGGTCGGGATGCAGATATGGAGTTGCCGAGT
ATTCTGATCAAGAATGAACCAGTGAGGAATCCTGCTAGAGAAATCCGTCA
AGTGGCAGAAGGAGCGCTCCGTCGATTCGAGCTGCTAGAACGGCAATATA
GGTATCTGGCTAACCAGCAAAGAG
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protein sequence of SMED30002730-orf-1

>SMED30002730-orf-1 ID=SMED30002730-orf-1|Name=SMED30002730-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=160bp
MPKLTAMNQDKCDVEMLENVRASAKKNKIMWGQTQTRWDEFDVTQMRSHE
GVHAEDHPAGGSSSQWSDVDRTTLTIPNRFVGMYRQALWDRGYYISTYDT
PEWPNRNSDGRDADMELPSILIKNEPVRNPAREIRQVAEGALRRFELLER
QYRYLANQQR
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head