SMED30033892

Overview
NameSMED30033892
Smed IDSMED30033892
Length (bp)521
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30033892 (SMED30033892) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033892 (SMED30033892) 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.
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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




SMED30033892

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



PAGE Curations: 17

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30033892SMESG000029612.1 SMESG000029602.1 SmedASXL_009684SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Category 3 cellSMED30033892SMESG000029612.1 SMESG000029602.1 SmedASXL_009684SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
whole organism asexual adult fluorescence in situ hybridization evidence
parenchymaSMED30033892SMESG000029612.1 SMESG000029602.1 SmedASXL_009684SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
whole organism asexual adult colorimetric in situ hybridization evidence
Smed sexual biotypeSMED30033892SMESG000070393.1 SMESG000040193.1 SMESG000029612.1 SMESG000029602.1 SMESG000019334.1 Contig13195uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000070393.1 SMESG000040193.1 SMESG000029612.1 SMESG000029602.1 SMESG000019334.1 Contig13195newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000037212.1 SMESG000029612.1 SMESG000029602.1 SMESG000028539.1 Contig12392uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000037212.1 SMESG000029612.1 SMESG000029602.1 SMESG000028539.1 Contig12392newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000040193.1 SMESG000029612.1 SMESG000029602.1 Contig13216uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000040193.1 SMESG000029612.1 SMESG000029602.1 Contig13216newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000029612.1 SMESG000029602.1 Contig12391uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000029612.1 SMESG000029602.1 Contig12391newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000056221.1 SMESG000046858.1 SMESG000029613.1 SMESG000029612.1 SMESG000029602.1 SMESG000025472.1 SMESG000023703.1 SMESG000011090.1 Contig36311uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000056221.1 SMESG000046858.1 SMESG000029613.1 SMESG000029612.1 SMESG000029602.1 SMESG000025472.1 SMESG000023703.1 SMESG000011090.1 Contig36311newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000081747.1 SMESG000063286.1 SMESG000053779.1 SMESG000029612.1 SMESG000029602.1 SMESG000029600.1 SMESG000018997.1 SMESG000009617.1 SMESG000005074.1 Contig43035uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033892SMESG000081747.1 SMESG000063286.1 SMESG000053779.1 SMESG000029612.1 SMESG000029602.1 SMESG000029600.1 SMESG000018997.1 SMESG000009617.1 SMESG000005074.1 Contig43035newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30033892SMESG000029612.1 SMESG000029602.1 SMED30026394smed_20140614PMID:26457503
Tu et al., 2015
whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30033892SMESG000029612.1 SMESG000029602.1 SMED30026394smed_20140614PMID:26457503
Tu et al., 2015
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033892 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.017297:13739..14229 -1973
v31.014125:14981..15471 +1955
v31.016335:11064..11509 +1948
v31.023086:6295..6740 +1912
v31.019011:9591..10036 -1885
v31.011531:13020..13597 +1882
v31.016398:10050..10498 -1874
v31.023086:1195..1829 +1858
Homology
BLAST of SMED30033892 vs. Planmine SMEST
Match: SMESG000029602.1 (SMESG000029602.1)

HSP 1 Score: 53.5286 bits (127), Expect = 2.528e-9
Identity = 61/67 (91.04%), Postives = 61/67 (91.04%), Query Frame = -1
Query:  150 GGPEXDRHRSRNXKKWFVDDALPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAGGPERDRPXSRN 350
            GGPE DRHRSRN KKWFVDDAL  AGGIVGGAADLAGGVVDGAANLAGAAIDVVAGGPERDR  SRN
Sbjct:   65 GGPERDRHRSRNDKKWFVDDALHLAGGIVGGAADLAGGVVDGAANLAGAAIDVVAGGPERDRHRSRN 131          
The following BLAST results are available for this feature:
BLAST of SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 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 SMED30033892 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000029602.12.528e-991.04SMESG000029602.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033892 ID=SMED30033892|Name=SMED30033892|organism=Schmidtea mediterranea sexual|type=transcript|length=521bp
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAGCTATAAAATATTTAT
TTTATAAAAAAGTATTCNCGTTNGATTCATTCGAGTTTAGGAAANGTTTG
TATTTTTACCTTGCTATTATGCAGCTTTGCTTATTACTGATTTCTTGGAA
TTTCGGGATCNGGGACGATCTCTTTCTGGACCNCCTGCTACTACATCTAT
TGCTGCNCCAGCAAGATTTGCAGCTCCATCAACGACTCCNCCTGCAAGAT
CTGCAGCTCCNCCAACGATTCCNCCTGCANGGGGTAAGGCATCATCTACA
AACCATTTCTTGNCATTTCGGGATCTATGACGATCNCTTTCTGGACCNCC
TGCTACTACATCTATTGCTGCNCCAGCAAGATTTGCAGCTCCATCAACGA
CTCCACCTGCAAGGNNGGCAGCTCCACCAACGATTCCNCCTGCNNGGNGT
NAGGCNTNNTCTACAANCCATTCTTGNNTTTNNGGGANCNATGNCNANCC
NNTTTNTGGGACCCCNGCTNC
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protein sequence of SMED30033892-orf-1

>SMED30033892-orf-1 ID=SMED30033892-orf-1|Name=SMED30033892-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=135bp
XXGVPXXXXXXXXXXQEWXVXXAXXXAXGIVGGAAXLAGGVVDGAANLAX
AAIDVVAXGPEXDRHRSRNXKKWFVDDALPXAXGIVXGAADLAXGVVDGA
ANLAXAAIDVVAXGPERDRPXSRNSKKSVISKAA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000035Category 3 cell
PLANA:0000421tail
PLANA:0002142parenchyma