SMED30024232

Overview
NameSMED30024232
Smed IDSMED30024232
Length (bp)672
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 SMED30024232 (SMED30024232) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024232 (SMED30024232) 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




SMED30024232

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30024232SMESG000047490.1 Contig2562newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30024232SMESG000047490.1 Contig2562uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30024232SMESG000062817.1 Contig2562newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30024232SMESG000062817.1 Contig2562uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
nervous systemSMED30024232SMESG000047490.1 dd_Smed_v4_707_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30024232SMESG000047490.1 dd_Smed_v4_707_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30024232SMESG000047490.1 dd_Smed_v4_707_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30024232SMESG000047490.1 dd_Smed_v4_707_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30024232SMESG000047490.1 dd_Smed_v4_707_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30024232SMESG000047490.1 Contig55449newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30024232SMESG000062601.1 SMESG000047490.1 OX_Smed_1.0.16988ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30024232 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.026726:541..3115 +3290
v31.018929:12957..15611 -3226
Homology
BLAST of SMED30024232 vs. Planmine SMEST
Match: SMESG000047490.1 (SMESG000047490.1)

HSP 1 Score: 132.109 bits (331), Expect = 1.054e-39
Identity = 83/91 (91.21%), Postives = 85/91 (93.41%), Query Frame = 2
Query:  365 FDSKFGLHSTNKSLVKRDWDYEYELIIPTTDAGERATLTKIFKENGFNVETTDSVIKGCSEDXXXXXXXXXXXXXXGFKVTLEKEELSYTF 637
            F S F ++ST   LVKRDWDYEYELIIPTTDAGERATLTKIFKENGFNVETTDSVIKGCSEDKAKAEALLATLKSKGFKVTLEKEELSYTF
Sbjct:    9 FLSIFQIYSTG--LVKRDWDYEYELIIPTTDAGERATLTKIFKENGFNVETTDSVIKGCSEDKAKAEALLATLKSKGFKVTLEKEELSYTF 97          
BLAST of SMED30024232 vs. Planmine SMEST
Match: SMESG000047488.1 (SMESG000047488.1)

HSP 1 Score: 46.595 bits (109), Expect = 6.167e-7
Identity = 37/85 (43.53%), Postives = 52/85 (61.18%), Query Frame = 2
Query:  365 FDSKFGLHSTNKSLVKRDWDYEYELIIPTTDAGERATLTKIFKENGFNVETTDSVIKGCSEDXXXXXXXXXXXXXXGFKVTLEKE 619
            F S F ++S    LVKRD D +Y LII T++  ER  L  +F ++ F++ET    I+G + +K+ AE L   L+ KGFKV  EKE
Sbjct:    9 FLSIFQIYSAR--LVKRD-DIDYILIINTSEESERLELIDVFVQSNFHIETDPKFIRGSTSEKSDAEDLKKKLEDKGFKVKFEKE 90          
The following BLAST results are available for this feature:
BLAST of SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 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 SMED30024232 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000047490.11.054e-3991.21SMESG000047490.1[more]
SMESG000047488.16.167e-743.53SMESG000047488.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024232 ID=SMED30024232|Name=SMED30024232|organism=Schmidtea mediterranea sexual|type=transcript|length=672bp
TGGCGTCGGATATTAAAGAATGTTAGTTATATAAATTTTACTTACAGAAA
TTAGTTGGAAATGTATTTTTAGTTATTCTAAAATTTATATCTTACGAAAT
ATTCTTCAATTCATAAAATTTATCATCTCTAAAAATACTTGAATAAATAT
TTTGTGCATAATATTACTTTTTAATAATCATCATTGCTGTTGACGATATT
ACACTATTTCCAGATTTAATGGGGTAAAAGCAAACAATATGTACGTCACA
CTCACTTGGCATTTTCGGCAATTGTATCAAAAATACATCAAATCGACATT
ATCTCAAAGTTTTATGCACATTGGTCATTTTTATAGACTTGGAAAGAACA
CGGTGTATTTTGATTTTGACTCAAAATTCGGACTGCATTCCACTAACAAG
TCACTTGTGAAAAGAGATTGGGATTATGAATATGAATTGATAATCCCGAC
TACCGACGCCGGGGAACGCGCAACTTTAACAAAAATATTTAAAGAAAACG
GATTCAATGTTGAAACGACAGATAGTGTGATCAAAGGCTGCAGCGAAGAT
AAAGCTAAAGCGGAAGCCTTATTGGCAACACTAAAAAGTAAAGGATTTAA
AGTGACATTAGAGAAAGAAGAGTTATCTTATACTTTTTAACTAAATGAAA
TTTTAAATAAATGAATTAGGAA
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protein sequence of SMED30024232-orf-1

>SMED30024232-orf-1 ID=SMED30024232-orf-1|Name=SMED30024232-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=134bp
MYVTLTWHFRQLYQKYIKSTLSQSFMHIGHFYRLGKNTVYFDFDSKFGLH
STNKSLVKRDWDYEYELIIPTTDAGERATLTKIFKENGFNVETTDSVIKG
CSEDKAKAEALLATLKSKGFKVTLEKEELSYTF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000418head