SMED30034824

Overview
NameSMED30034824
Smed IDSMED30034824
Length (bp)1022
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 SMED30034824 (SMED30034824) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034824 (SMED30034824) 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 SMED30034824 (SMED30034824) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034824 (SMED30034824) 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



SMED30034824

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
protonephridiaSMED30034824SMESG000035183.1 dd_Smed_v4_951_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30034824SMESG000035183.1 dd_Smed_v4_951_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034824SMESG000035183.1 dd_Smed_v4_951_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034824SMESG000035183.1 Contig51205newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034824SMESG000035183.1 Contig51205uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30034824SMESG000035183.1 dd_Smed_v6_951_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30034824SMESG000035183.1 dd_Smed_v4_951_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30034824SMESG000035183.1 dd_Smed_v4_951_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30034824SMESG000035183.1 dd_Smed_v4_951_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30034824 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000247:70755..71654 -2650
Homology
[Close]
BLAST of SMED30034824 vs. TrEMBL
Match: A0A267FEU5 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig019061g1 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 2.826e-8
Identity = 30/62 (48.39%), Postives = 39/62 (62.90%), Query Frame = 1 
Query:  136 VQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFKLQKKPRRTR 321
            V+SVTL++GK NP  YI YDT E N  +H+ +S+ I +AIL  IW  V    KL  K R+ R
Sbjct:   18 VRSVTLQEGKSNPQKYIYYDTDEFNPWIHLAISLPILYAILIFIWSGVTLYMKLSGKSRQRR 79
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BLAST of SMED30034824 vs. TrEMBL
Match: A0A267DR65 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig017648g1 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.037e-7
Identity = 29/62 (46.77%), Postives = 38/62 (61.29%), Query Frame = 1 
Query:  136 VQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFKLQKKPRRTR 321
            V+ VTL++GK NP  YI YDT E N  +H+ +S+ I +AIL  IW  V    KL  K R+ R
Sbjct:   19 VRGVTLQEGKSNPQKYIYYDTDEFNPWIHLAISLPILYAILIFIWSGVTLYMKLSGKSRQRR 80
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BLAST of SMED30034824 vs. TrEMBL
Match: A0A0R3T5A7 (Uncharacterized protein OS=Rodentolepis nana OX=102285 GN=HNAJ_LOCUS2243 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 3.313e-7
Identity = 32/72 (44.44%), Postives = 42/72 (58.33%), Query Frame = 1 
Query:  124 FTFKVQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFK-LQKKPRRTRTYESH 336
             T  + ++TLE+G  N   YI YDTS  N G+H GL++LITF IL      V AI K L+K+ +R     SH
Sbjct:   15 LTHMISAITLEEGMANKDKYIFYDTSSFNAGIHAGLALLITFGILGTFTSTVMAITKALEKRRKRHTLTTSH 86
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BLAST of SMED30034824 vs. TrEMBL
Match: G7YQP5 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CLF_107516 PE=4 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 7.255e-7
Identity = 29/63 (46.03%), Postives = 41/63 (65.08%), Query Frame = 1 
Query:  136 VQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFKLQKKPRRTRT 324
            VQ VTLE+G +NP  YI YD +  N+G+H G+S+LIT++IL I+   +  I +     RR RT
Sbjct:   16 VQMVTLEEGLKNPEKYIFYDQNPFNIGMHAGISLLITYSILAIVLTFITIISRALGY-RRKRT 77
[Close]
BLAST of SMED30034824 vs. TrEMBL
Match: A0A183PI93 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS14079 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 3.983e-6
Identity = 23/42 (54.76%), Postives = 32/42 (76.19%), Query Frame = 1 
Query:  136 VQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILT 261
            VQ VTLE    +P  YI+YDTS+ N+G+H+GLS+LI + IL+
Sbjct:   18 VQMVTLEQAMSDPDKYIRYDTSDFNIGMHVGLSLLINYGILS 59
[Close]
BLAST of SMED30034824 vs. Planmine SMEST
Match: SMESG000035183.1 (SMESG000035183.1)

HSP 1 Score: 156.762 bits (395), Expect = 7.554e-48
Identity = 91/91 (100.00%), Postives = 91/91 (100.00%), Query Frame = 1 
Query:   67 MTFWXXXXXXXXXXXXXSFFTFKVQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFKLQKKPRRTRTYESHL 339
            MTFWLVMRLNLLLLSILSFFTFKVQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFKLQKKPRRTRTYESHL
Sbjct:    1 MTFWLVMRLNLLLLSILSFFTFKVQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFKLQKKPRRTRTYESHL 91
[Close]
BLAST of SMED30034824 vs. Planmine SMEST
Match: SMESG000022725.1 (SMESG000022725.1)

HSP 1 Score: 54.6842 bits (130), Expect = 8.705e-10
Identity = 25/56 (44.64%), Postives = 37/56 (66.07%), Query Frame = 1 
Query:  136 VQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFKLQK 303
            V+ VTL    + P +YIKYD +   +  HIG+S+ I +AIL  IW +VN IFK+++
Sbjct:    4 VKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIWSMVNLIFKIRE 59
The following BLAST results are available for this feature:
BLAST of SMED30034824 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 SMED30034824 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 SMED30034824 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 SMED30034824 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 SMED30034824 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 SMED30034824 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 SMED30034824 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 SMED30034824 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267FEU52.826e-848.39Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267DR651.037e-746.77Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A0R3T5A73.313e-744.44Uncharacterized protein OS=Rodentolepis nana OX=10... [more]
G7YQP57.255e-746.03Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
A0A183PI933.983e-654.76Uncharacterized protein OS=Schistosoma mattheei OX... [more]
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BLAST of SMED30034824 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 SMED30034824 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 SMED30034824 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 SMED30034824 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 SMED30034824 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 SMED30034824 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000035183.17.554e-48100.00SMESG000035183.1[more]
SMESG000022725.18.705e-1044.64SMESG000022725.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034824 ID=SMED30034824|Name=SMED30034824|organism=Schmidtea mediterranea sexual|type=transcript|length=1022bp
TGCGTGATGATGTGCTCTCCGTGTTATTTTAAATTGACGCATAAATAGTG
AGCAAAACTCATTTGTATGACATTTTGGTTAGTGATGAGGTTGAATTTGT
TGCTTTTGTCGATTTTGTCGTTTTTTACATTCAAAGTCCAATCAGTTACT
TTGGAAGATGGAAAACAGAATCCGGGGCTCTACATCAAGTACGACACTTC
GGAAATGAATCTTGGATTACATATTGGCTTGTCAATATTAATAACGTTCG
CCATTCTAACAATAATCTGGTGCATTGTCAATGCCATTTTCAAATTGCAA
AAGAAACCAAGGCGAACAAGGACATACGAAAGCCATTTGTGAAAGTGAAG
TTGGAAATAAGTTTGACTTTCAAGTTTAGTTCAGAAATTATCGAAATATT
CTAACGATTTTCAGAAGTTATTTGTATATGAAATGATTTAATAAATGTAT
TTTATTTAAAAAAAANANAAATTATAACAAATATGCATTTTTATAATATC
CCCTAACTACTCTCTGAACTTTATTCTTCATAATGCGTCTCTCGTTTTCG
CTAAACATAGTAACTGAGCTAGCATCGCTCCAACTTGTGAGGAACTGAAT
TATGTTCCTTCTAATTTTTATATATAGTGTTTTGTTTCAATTAGTTAAGT
CTTTTGATCTATTGGTCGAAGAACTCTGAACAAAATGGCATTCCAATCAC
GTTCATTCTAAAATAGTCATCACATTCCCATATGATAATTTGTATTCATT
CATTTATCCCACTTCCAATTCTCGATCTTACTAGGATTTTAGCGATCGCC
TATCATCTTTTTCAGAGTTTCTCCTGAGTACATTACGTCGGGGTTGTAGA
CATAAGAAAAGTGGCCACTCGTTTCTGTAAGACTCTTACTTTCGGTATGG
CTGCAGACCTAGATGTAACTGTTCATTTTTCGGTCAACGGAGCTGAATGT
TGCCTGGCAAATTATTTCATTTAAACTTATTTGAATTCTAATATTAAATC
GGCAAATCATATGTCGTGGTCA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0002032epidermal cell
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-TMSignalP-TMcoord: 1..26
score: 0.68
NoneNo IPR availableTMHMMTMhelixcoord: 53..75
NoneNo IPR availableTMHMMTMhelixcoord: 7..29