SMED30032042

Overview
NameSMED30032042
Smed IDSMED30032042
Length (bp)396
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 SMED30032042 (SMED30032042) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30032042 (SMED30032042) 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 SMED30032042 (SMED30032042) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30032042 (SMED30032042) 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



SMED30032042

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30032042h1SMcG0002112 SmedASXL_006770SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30032042h1SMcG0002112 dd_531dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
pharynxSMED30032042h1SMcG0002112 dd_Smed_v4_531_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30032042h1SMcG0002112 dd_Smed_v4_531_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30032042h1SMcG0002112 dd_Smed_v6_531_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30032042h1SMcG0002110 Contig43504uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30032042h1SMcG0002110 Contig43504newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30032042h1SMcG0002112 Contig43504uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30032042h1SMcG0002112 Contig43504newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30032042 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014976:11676..12078 -1944
v31.014976:161..563 -1917
v31.003943:9991..10393 +1899
v31.021666:10893..11288 -1828
Homology
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BLAST of SMED30032042 vs. Planmine SMEST
Match: SMESG000065349.1 (SMESG000065349.1)

HSP 1 Score: 223.016 bits (567), Expect = 1.034e-76
Identity = 114/114 (100.00%), Postives = 114/114 (100.00%), Query Frame = 3 
Query:   30 IKLVTLILNILDYYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQQNNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL 371
            IKLVTLILNILDYYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQQNNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL
Sbjct:    6 IKLVTLILNILDYYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQQNNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL 119
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BLAST of SMED30032042 vs. Planmine SMEST
Match: SMESG000065355.1 (SMESG000065355.1)

HSP 1 Score: 196.823 bits (499), Expect = 1.166e-65
Identity = 98/102 (96.08%), Postives = 100/102 (98.04%), Query Frame = 3 
Query:   66 YYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQQNNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL 371
            YYTTS YNR YRTTPPTNNK+ARLESLLQNIYSRLNYLQTIINQ+NNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL
Sbjct:   68 YYTTSLYNRNYRTTPPTNNKIARLESLLQNIYSRLNYLQTIINQKNNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL 169
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BLAST of SMED30032042 vs. Planmine SMEST
Match: SMESG000065350.1 (SMESG000065350.1)

HSP 1 Score: 198.749 bits (504), Expect = 5.453e-64
Identity = 97/102 (95.10%), Postives = 100/102 (98.04%), Query Frame = 3 
Query:   66 YYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQQNNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL 371
            YYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQ+NNRNGPLLGYLRRIVPSYRRSLVQINRKYC +YSANK LC+LIRDVQLVLNRVSRFL
Sbjct:  250 YYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQKNNRNGPLLGYLRRIVPSYRRSLVQINRKYCEQYSANKELCKLIRDVQLVLNRVSRFL 351
[Close]
BLAST of SMED30032042 vs. Planmine SMEST
Match: SMESG000065350.1 (SMESG000065350.1)

HSP 1 Score: 197.978 bits (502), Expect = 3.584e-62
Identity = 97/102 (95.10%), Postives = 100/102 (98.04%), Query Frame = 3 
Query:   66 YYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQQNNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL 371
            YYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQ+NNRNGPLLGYLRRIVPSYRRSLVQINRKYC +YSANK LC+LIRDVQLVLNRVSRFL
Sbjct:  401 YYTTSWYNRYYRTTPPTNNKVARLESLLQNIYSRLNYLQTIINQKNNRNGPLLGYLRRIVPSYRRSLVQINRKYCEQYSANKELCKLIRDVQLVLNRVSRFL 502
[Close]
BLAST of SMED30032042 vs. Planmine SMEST
Match: SMESG000065348.1 (SMESG000065348.1)

HSP 1 Score: 51.9878 bits (123), Expect = 8.230e-9
Identity = 24/60 (40.00%), Postives = 37/60 (61.67%), Query Frame = 3 
Query:  192 NQQNNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYSANKGLCQLIRDVQLVLNRVSRFL 371
            N   N++  L+ YLRR+VP+Y+R +   NR  C  Y  +   C++IRD+Q  L  ++RFL
Sbjct:  135 NNGKNKSSQLIRYLRRVVPNYQRKISLWNRTNCRTYRRSSDFCKIIRDIQSSLGDIARFL 194
The following BLAST results are available for this feature:
BLAST of SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 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 SMED30032042 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000065349.11.034e-76100.00SMESG000065349.1[more]
SMESG000065355.11.166e-6596.08SMESG000065355.1[more]
SMESG000065350.15.453e-6495.10SMESG000065350.1[more]
SMESG000065350.13.584e-6295.10SMESG000065350.1[more]
SMESG000065348.18.230e-940.00SMESG000065348.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032042 ID=SMED30032042|Name=SMED30032042|organism=Schmidtea mediterranea sexual|type=transcript|length=396bp
GAATGACAATCAAGAGAAACAATGTTTATATCAAACTAGTTACTTTAATA
TTAAATATTCTAGATTATTACACAACTTCTTGGTACAATCGCTACTACAG
AACGACTCCACCAACTAATAACAAAGTTGCGAGATTAGAAAGTCTTCTAC
AGAACATTTATTCAAGACTCAATTATCTACAGACGATAATTAATCAACAA
AATAACAGAAATGGACCACTTTTGGGTTATTTAAGAAGAATTGTTCCAAG
TTATCGCCGGTCATTGGTGCAAATCAACAGGAAATATTGTGGGCGATATA
GTGCAAATAAAGGACTCTGTCAATTGATCCGAGACGTGCAACTTGTTCTG
AACAGAGTTTCACGATTTCTGTAGTAACAAATAAAATTTAGAATAA
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protein sequence of SMED30032042-orf-1

>SMED30032042-orf-1 ID=SMED30032042-orf-1|Name=SMED30032042-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=124bp
MTIKRNNVYIKLVTLILNILDYYTTSWYNRYYRTTPPTNNKVARLESLLQ
NIYSRLNYLQTIINQQNNRNGPLLGYLRRIVPSYRRSLVQINRKYCGRYS
ANKGLCQLIRDVQLVLNRVSRFL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000420parapharyngeal region
PLANA:0002089reproductive organ