SMED30001670

Overview
NameSMED30001670
Smed IDSMED30001670
Length (bp)346
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 SMED30001670 (SMED30001670) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001670 (SMED30001670) 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 SMED30001670 (SMED30001670) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001670 (SMED30001670) 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



SMED30001670

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



PAGE Curations: 42

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
posterior region of the whole animalSMED30001670h1SMcG0007041 dd_Smed_v4_2442_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 dd_Smed_v4_2442_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30001670h1SMcG0007041 dd_Smed_v4_2442_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
mouthSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
central nervous systemSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
central nervous systemSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult fluorescence in situ hybridization evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult fluorescence in situ hybridization evidence
parapharyngeal regionSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
tail regionSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
tail regionSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
cholinergic neuronSMED30001670h1SMcG0007041 SmedASXL_008878SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult fluorescence in situ hybridization evidence
central nervous systemSMED30001670h1SMcG0007041 SMED30032613smed_20140614PMID:27034770
Currie et al., 2016		whole organism asexual adult fluorescence in situ hybridization evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 SMED30032613smed_20140614PMID:27034770
Currie et al., 2016		whole organism asexual adult fluorescence in situ hybridization evidence
cholinergic neuronSMED30001670h1SMcG0007041 SMED30032613smed_20140614PMID:27034770
Currie et al., 2016		whole organism asexual adult fluorescence in situ hybridization evidence
tail regionSMED30001670h1SMcG0007041 SmedASXL_015539SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:25725068
Owen et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30001670h1SMcG0007041 dd_Smed_v4_2442_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30001670h1SMcG0007041 dd_Smed_v4_2442_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30001670h1SMcG0007041 dd_Smed_v4_2442_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30001670h1SMcG0007041 dd_Smed_v4_2442_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001670h1SMcG0007041 Contig42541newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001670h1SMcG0007041 Contig42541uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
tail regionSMED30001670h1SMcG0007041 dd_Smed_v6_2442_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:21806978
Iglesias et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
mouthSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:21806978
Iglesias et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:21806978
Iglesias et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:21282632
Almuedo-Castillo et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
mouthSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:21282632
Almuedo-Castillo et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:21282632
Almuedo-Castillo et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
tail regionSMED30001670h1SMcG0007041 OX_Smed_1.0.12463ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
mouthSMED30001670h1SMcG0007041 EU082824smed_ncbi_20240424PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 EU082824smed_ncbi_20240424PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
mouthSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:20422023
Felix et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
mouthSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:20422023
Felix et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
posterior region of the whole animalSMED30001670h1SMcG0007041 EU082824.1smed_ncbi_20240424PMID:20422023
Felix et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001670 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.024755:5374..5720 -1709
Homology
The following BLAST results are available for this feature:
BLAST of SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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 SMED30001670 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

>SMED30001670 ID=SMED30001670|Name=SMED30001670|organism=Schmidtea mediterranea sexual|type=transcript|length=346bp
AAAAATTAATCAATTTAAACAAAAAAAAATTCAACTATTGTATATAGTCA
ATACAGCCAATGGATAAATTGGTACTGCTATTTTTATTATTTCGATGTAT
CAATACGACTAAACAAAATGACAAACGATAATGAGTAATATTTATTAATA
GGTTTGTTTGGAGATAATTTTTTATGCTTTCATATTGGTGCGGCAAGTCG
TTTGATTTTTGTAAATTTTTTGTTTTATTATATAAAGCTTTATATTAGTT
ATCGGGTACATCTTATCGGCGATATTTTGATTATAGATTTGTTTGATTGG
CTGATTTTGTCGAAAATAGAGATATACGCTTTTCAATCGATACAAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000421tail