SMED30023308

Overview
NameSMED30023308
Smed IDSMED30023308
Length (bp)2489
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 SMED30023308 (SMED30023308) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023308 (SMED30023308) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 SMED30023308 (SMED30023308) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023308 (SMED30023308) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top


 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30023308

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



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30023308SMESG000063568.1 Contig657newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023308SMESG000028901.1 Contig657newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30023308SMESG000063568.1 dd_Smed_v4_762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30023308SMESG000063568.1 dd_Smed_v6_762_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
intestinal phagocyteSMED30023308SMESG000063568.1 dd_Smed_v6_762_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gamma neoblastSMED30023308SMESG000063568.1 dd_Smed_v6_762_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
Alignments
SMED30023308 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001483:9386..11873 -12203
Homology
The following BLAST results are available for this feature:
BLAST of SMED30023308 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023308 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023308 ID=SMED30023308|Name=SMED30023308|organism=Schmidtea mediterranea sexual|type=transcript|length=2489bp
TTATTTTAGAAATCTAATCGTGATTTAATATTTAAACAATAATATTGATA
TCACCGAGAATGTATTACAAAAGGGTGAAGGGGTTCGAGCTCTTGCATTA
TTCTGGTTTGGGTATAATTGCATAAACAGATTCCTATTTCAAAGAAAGAG
AAATCTGAATAATACATTAGATAAACGACATAATGTTGAATGGACGCAAT
TTCACAGGGAATGGCCATAAATAATTAGCGTAATTTCCAGTCATAGATAA
TTTATTATATATTGCTTGTCTACAGTCTAATTCAGCCCAATCATCTTATC
ACATTTATAATCCCCATCTTTCTATAAAATTGCTTTCCTTTGTCCCAAAA
ATTTGACATATCCCAAAGTCACAAAATCCCCATTTCAAATCGATGCCTAA
GTAATAAAATAGAAATCCTTAAAGCCGTAAAACTTCCATTTAGTTGTAAA
CAATGGGAACATCATAATGGACATATCGTCCTTACTGTTGGACTAGTTAT
TCAAATGCAAATTTCTAGCCGCGCTGCTGCTGTAGGACCTTAACAATACG
TTCTGGACACAAATGATGTACACACATACCGCGCACACACAAGCATCAAC
ATGGAATGTAACAAATGATTTTCGACCAATCAGAATCAGGTCTCAAAGTT
CAAATTCCACAGTATAATTGAGCTGTTTTAGTGTTACGTATCATTGAATT
GATTTCTAAAATGGGAAAGGAATTAGAGGAATTAAACAATGAGGCCTTGG
AAAAACATAATGAGTAAGTTCTTCACTTTGTTTGTTTATATTTTATTCAC
TTATGATGCTGATTTGTGATGTAATGTTTGCTGCTTGATTGCGTAACCAA
TAAAAATCTAACTACAAATCACTAATTTCCATATTCAAATAATCGATTCC
AATCTCATTGAGAATTCAAATTCAAGTTTTAATGAAATTATCGATTAAAT
GTGCAAAATCAATAATTTTAAAATGGTATCTATAGATATCGAAAGTTCTG
AAATTAATTTAGTTTGAATTTATTCGCTTTGTATTTCTATAATTTCACGA
AATTATATTAAAAGTATGATATAAACCGAGTTTAGACCGGTAGTTGACGG
TGGAAACGCATTTTTAACGGAAATTTATGAGCGACCGAATTTTGGAAAAT
TTTGCATATTATTGGTAAGATAACAGAAAACGAAGAATGAAATAAAATGG
AAAAATCAAGCTAAAATATAAGATATTCACTACTAAGATAAGTCAAAACA
ATTAACAATAGTGAGAGCTAATGTAGTCCCGTGAAGGCTTCTATACGAAA
TATCTTCATTTTATTGTTATTTGGACTCAAGTCATTACAAACCTAATACA
AAAGTTTATGAAATAAGTTATAAAATCACAAAACCTGTCACAGATTCGGT
AAGTCTGTAGGGCAATTCACAATTTCAGGGGCTATGAAGATATCTAAAAC
GAATCGTTAATTCCATTCGTCATGAAATCATGTAGATCTTTATAATTTTT
TATCTTATTTGAAATAAACAAATATTGCTTGCCAGCTTTGTTTTAATATT
CCAGTGTCCACATGTTTTAACCACTCCATATAAGTAACAGCTTGAAAACT
CGTTCACCTAATAATAAATAGTTTCTTAATGTCTGTTCCAGATCCACTTC
CAATATGGAAGTAATGCATTTTATTGAAGAAGGTTTCTTAATTACCACCC
AAACGAATCTTTAAAGCCCGTTTTCCTATCTGAACTCAATATTTTTAATT
TCCTAATAATTTTAAGCCCGTGAAATATTTTTCTGCTTTGTTACTGAAAA
GTATTTTCACACAAACTCAAGAAGAAATTGAAATACATATGAAAGCTATA
AAACAGATATCAGGCTCTTTTCCTTGTTTTTCTCGTTATCCAGACGTACG
ATAAATATTTATAAACAAGACGAAGAGCATTAGGAAATCTTTTCATTCTA
TTAGAAAGCCAAAAGTAGGCAACTCGTCTCCCTGCTTTCTCAAATTATAA
ATTAATCAAAATAGCAATAAGGGAGATTTATAAAATATTTCAAGCCCACA
TAGAGCGCTCTTGATTATACAAGCCGCAAACAGAACAGATGGTACTTTTT
ATCAAAGAGTCATTTCCAGATGTCTTGAAAAAAATGATTATTTAACGTGG
AAATAAGGGCTACTATGTGAGACGGCAGTGTGGGTCTTCGTAAATGATCT
AATATCCGGTTCTGTATTAGTTATATTTTTTTCTATAATTTATTTGAACA
GATAAAATTTTCCATTTTCCACTTATTGAATGGAAATATTTTATTTAATG
ATTGTTGGCTAGATTTTCAATTAGTGAAGGCCAATCTTGAAAGCCGCTGA
CGAGGGGATATAATGACCGGCTATTGAGATAATAGATTTGCTATTAATAA
TATATTTATTATTTCAAATGATGGAGGATAAATGCAGCAATTATATTAAT
GTTTACAGTGATTATAAAAGATAATAATTTCAATAATAA
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000026gut
PLANA:0000028Category 2 cell
PLANA:0000039gamma neoblast
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0002032epidermal cell
PLANA:0003001lateral region of the whole animal
PLANA:0003117parapharyngeal cell