SMED30031573

Overview
NameSMED30031573
Smed IDSMED30031573
Length (bp)472
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 SMED30031573 (SMED30031573) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031573 (SMED30031573) 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 SMED30031573 (SMED30031573) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031573 (SMED30031573) 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




SMED30031573

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30031573SMESG000060425.1 Contig2599newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031573 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004643:7881..8353 +2277
v31.004204:25684..26156 -2250
v31.005877:6312..6784 +2187
v31.003678:42165..42637 +2178
v31.009356:15442..15914 -2169
v31.008751:12671..13142 +2143
v31.001873:42279..42752 -2084
v31.004027:25455..25941 +1914
v31.000046:183103..183588 -1913
v31.007880:18524..19011 -1869
v31.001301:100936..101421 -1860
v31.001950:47453..47940 +1852
v31.004935:46173..46657 -1851
v31.023287:5105..5585 +1840
v31.004102:14287..14767 -1837
v31.020484:4768..5251 -1824
v31.004077:31008..31506 +1815
v31.034434:1254..1735 -1806
v31.011165:4488..4928 -1793
v31.001655:57006..57492 +1793
v31.006121:40163..40650 +1790
v31.003515:41344..41821 -1779
v31.006631:26240..26726 -1757
v31.004885:8819..9259 -1748
v31.004072:40155..40633 -1689
v31.000761:94811..95296 -1689
v31.000570:96678..97163 +1670
v31.013574:7870..8355 +1661
v31.003645:56701..57186 -1661
v31.021682:4072..4557 -1653
v31.012826:13375..13859 -1652
v31.005871:38712..39197 -1652
v31.001449:40980..41464 -1648
v31.002573:30775..31255 -1647
v31.006412:20889..21374 +1644
v31.006940:366..851 -1643
v31.000702:5038..5524 -1639
v31.003724:8798..9283 -1634
v31.000058:141894..142380 +1632
v31.005759:7110..7590 -1629
v31.000935:44436..44921 +1629
v31.000192:43469..43955 -1622
v31.000902:44722..45207 +1616
v31.000706:44778..45262 +1602
v31.001069:50496..50983 -1601
v31.000750:120849..121327 +1599
v31.003339:56398..56883 +1598
v31.000194:82758..83239 -1588
v31.007381:24867..25353 -1586
v31.005096:26774..27249 +1582
v31.002256:6781..7264 -1579
v31.000841:57597..58045 +1383
v31.000132:14061..14513 +1282
Homology
The following BLAST results are available for this feature:
BLAST of SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 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 SMED30031573 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031573 ID=SMED30031573|Name=SMED30031573|organism=Schmidtea mediterranea sexual|type=transcript|length=472bp
GTTCGCGGCAGATATTTCTTCGGCGTCATGATCTTGTTTGGTCAATGTCA
TTGACCATCGTCCGCGTTGGAATGTAGTCTGTTTACTCTGTCACAAACTG
TCTGTAGTTTATCTATTTATATTGCCATTGCGATCGAATTTGCTCTCTAT
TGGTTTCGTGGATTATTACATGGCCAATTTTATTGTTAATTCGGTAAATG
GATTTCTAGGATGTTCTCTCTCTGAATTATTGCTCTTATTCAACGACGGC
TAACTAGGAATTCACTCTATTAAGATTTACTCCGGATTATGCTGTTTTCG
AAAATGTTCAATGGTACGTGCTCGTCATGGAGAAGACTACTAGGTGAGAT
ACTCAACGACTGCGATTCGATGAAGAGTATGCTAGGGTTGTGGTGGAGCC
TAAATCTTTGCTCTATATATGATCTACTATTTCATTGCGTTGTGATGTTA
AATTATATTGTTCGCTAATTTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte