SMED30034101

Overview
NameSMED30034101
Smed IDSMED30034101
Length (bp)1436
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 SMED30034101 (SMED30034101) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034101 (SMED30034101) 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 SMED30034101 (SMED30034101) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034101 (SMED30034101) 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




SMED30034101

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
pharynxSMED30034101 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30034101 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034101 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30034101 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30034101 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30034101 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30034101 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30034101 dd_Smed_v6_3534_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
musculature systemSMED30034101 dd_Smed_v6_3534_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30034101 vs. Planmine SMEST
Match: SMESG000055984.1 (SMESG000055984.1)

HSP 1 Score: 47.3654 bits (111), Expect = 7.980e-9
Identity = 23/37 (62.16%), Postives = 27/37 (72.97%), Query Frame = 2
Query: 1043 VSGYFINDRHDLIVNKLVAHASSWLIFHHNFCRSELD 1153
            + GYFI+DRHDL VN LV      +IFH+NF RSELD
Sbjct:    1 MPGYFISDRHDLTVNSLVDCGFVVVIFHNNFSRSELD 37          

HSP 2 Score: 31.5722 bits (70), Expect = 7.980e-9
Identity = 15/27 (55.56%), Postives = 18/27 (66.67%), Query Frame = 1
Query: 1171 PFHVPHSRRTPITPRF*TSLRMTFMRR 1251
            P  +  + +TPITPR   S RMTFMRR
Sbjct:   60 PVWIILAEQTPITPRLWISFRMTFMRR 86          
BLAST of SMED30034101 vs. Planmine SMEST
Match: SMESG000078452.1 (SMESG000078452.1)

HSP 1 Score: 47.3654 bits (111), Expect = 2.427e-6
Identity = 22/37 (59.46%), Postives = 27/37 (72.97%), Query Frame = 2
Query: 1043 VSGYFINDRHDLIVNKLVAHASSWLIFHHNFCRSELD 1153
            +SGYFI+DRHDL +N LV       IFH+N+ RSELD
Sbjct:   61 MSGYFISDRHDLTMNNLVGGGFVVAIFHNNYSRSELD 97          
The following BLAST results are available for this feature:
BLAST of SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 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 SMED30034101 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000055984.17.980e-962.16SMESG000055984.1[more]
SMESG000078452.12.427e-659.46SMESG000078452.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034101 ID=SMED30034101|Name=SMED30034101|organism=Schmidtea mediterranea sexual|type=transcript|length=1436bp
ACTACATAGGGATTATGGCTTCCACGGGGGTTGTGTTACCGAGTTTGTTA
AAGAAACCATTGCTTAAACTCCTTGCTTGGGATTACTACATCTGATCTCA
CGACGTGGTCGACTCAGCTCGTGTTGTATTCATTTCATTTTTTCGGCAAC
GAAAACCTTGATGGTGAAGTAATTTATTTCTGGTTGCAGTAACGTTCGCA
TGTTTTAGTGTTATCTAGATTGAATAAAACGCACGGATACTGGTGTGGCT
GGTTGATTCAAATGGACAACAAGTGATTAACAGGCGATTAGTTGGTGAGA
GTGATACGAGTATTTCACGACATGTCCTATCGTTTATCTGAACGGTGATA
AGCACCGTAAGAGGCGACGTTTATGGAGGCTACAGAGTCGTCATTTGCTT
GCGATTTCGCTATCTTAGAATTTTCTGAGTTCCGATCCCAAGTGGGGCAA
AGTGCGTAATCAACGGCCTTACTAGTGATTTTTCTCCGGTTGTCTTTATA
CATCATTCAAACAATTCGTTGAGGAATAAAACATTTATATTCAAAAAATC
AATGCATAATCCATAAGTCGATGGGTCCGGGTCTGCGGCTTGCATTCTGG
ATGGGATTTTTTCTGGGTATCGGTCACGTTTGGTGATCGTTGCGGTTGGA
AATTTTTCGTTCTATTGTAATTTCATCGTCTGGGGTTCCTCGTAACTTGA
CTGAGCCTCCGTGTATCGGGTATCTATAATTGGATTGCATAATTTCAGCT
GTAACTATACGCAAAATGACGGCACCCAGACTAGAGGTGGAATTTATATG
CGTATGAGTGTCTTTTCTGTGTCAGTTTGGGTACGGGTGTGCATCAAATT
ATTGTTGCACACTATCTCTGTTTTAAATGGCTTTCACTGGAAATGCGTAG
GCGGAATTCCATCTGACTATGTTGGCTGGGTAGATATTCGATCGATTGAT
GACAGATAAATGTCAGGTCGCATGCGCCCGGTTCTGATTTATTTATTTGG
ATTTTCATACTTATCAGAATTCTTATATGGTGATTGATAATTGTGTCAGG
GTATTTCATTAACGATCGGCATGATTTGATAGTGAACAAGTTGGTGGCTC
ATGCATCATCGTGGCTAATTTTTCATCATAACTTTTGTCGCTCTGAGTTG
GACAATTTATCATACTTGTCCCTTTCCACGTGCCTCATTCGAGACGGACT
CCTATTACGCCTCGATTCTAGACCTCCCTTAGGATGACTTTTATGAGACG
TGAATGATTATAATTCGGAGTGGGCAGAGTCGGAGCAATATAATTTCTTC
AAATCAATGTTTGTCATGGCATTTCTTTGTTCTTATGTTTATTGAATACT
CTTTTTTCATGTGTTTTGATTCATAAATATGTTTGTTCCTAATGTTTTGA
AAAGTCAGCTTTCTGGGCAATAATGGTTTTTGTTCT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000428musculature system
PLANA:0000478pharynx musculature