SMED30027463

Overview
NameSMED30027463
Smed IDSMED30027463
Length (bp)195
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30027463

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



PAGE Curations: 23

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30027463h1SMcG0002430 Contig48789newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027463h1SMcG0002430 Contig48789uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
testisSMED30027463h1SMcG0002430 DN309082.1smed_ncbi_20240424PMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite fluorescence in situ hybridization evidence
spermatocyteSMED30027463h1SMcG0002430 DN309082.1smed_ncbi_20240424PMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite fluorescence in situ hybridization evidence
head regionSMED30027463h1SMcG0002430 OX_Smed_1.0.03975ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
enteric muscle cellSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
testisSMED30027463h1SMcG0002430 PL08010A1B05smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
reproductive organSMED30027463h1SMcG0002430 Contig21688uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30027463h1SMcG0002430 Contig21688newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
testisSMED30027463h1SMcG0001011 Contig3817GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30027463h1SMcG0002430 Contig3817GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
reproductive organSMED30027463h1SMcG0002430 Contig54410newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30027463h1SMcG0002430 Contig54410uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Category 2 cellSMED30027463h1SMcG0002430 dd_Smed_v4_2911_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
testis primordiumSMED30027463h1SMcG0002430 Contig3817_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism juvenile stagecDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027463 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.020940:854..1501 +949
Homology
The following BLAST results are available for this feature:
BLAST of SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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 SMED30027463 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

>SMED30027463 ID=SMED30027463|Name=SMED30027463|organism=Schmidtea mediterranea sexual|type=transcript|length=195bp
ATGAAATCATTTTATATGGCGGGGATAAATTCTACAAGAATCATTAAAGA
GAAAATATTTAATTTTTGTAAAACTTTTCTGAGTAATATCTCTACAATAT
CTCTAAATTCTTTGCTAATTGTGTTCAATACCGTTGAACATTATAAACAT
AAAAGAAAGAAATCAATGCAACGCGATAATGAAGAGAATGAAGAC
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 41..53
NoneNo IPR availableTMHMMTMhelixcoord: 13..35