SMED30011862

Overview
NameSMED30011862
Smed IDSMED30011862
Length (bp)481
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 SMED30011862 (SMED30011862) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011862 (SMED30011862) 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 SMED30011862 (SMED30011862) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011862 (SMED30011862) 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



SMED30011862

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
neoblastSMED30011862h1SMcG0006253 SMED30019097smed_20140614PMID:29906446
Zeng et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pigment cellSMED30011862h1SMcG0006253 SmedASXL_013552SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30011862h1SMcG0006253 SmedASXL_013552SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30011862h1SMcG0006253 SmedASXL_013552SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30011862h1SMcG0006253 SmedASXL_071363SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
protonephridiaSMED30011862h1SMcG0006253 dd_Smed_v4_7227_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30011862h1SMcG0006253 dd_Smed_v4_7227_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011862h1SMcG0006253 dd_Smed_v4_7227_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30011862h1SMcG0006253 dd_Smed_v4_7227_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30011862h1SMcG0006253 dd_Smed_v4_7227_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011862h1SMcG0006253 Contig37301uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011862h1SMcG0006253 Contig37301newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011862h1SMcG0006253 Contig3942newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011862h1SMcG0006253 Contig3942uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
sigma neoblastSMED30011862h1SMcG0006253 SMED30019097smed_20140614PMID:30194301
Mihaylova et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
sigma neoblastSMED30011862h1SMcG0006253 JQ425151smed_ncbi_20240424PMID:30194301
Mihaylova et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 SMED30019097smed_20140614PMID:28072387
Davies et al., 2017		whole organism Stage 8 colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 SMED30019097smed_20140614PMID:28072387
Davies et al., 2017		whole organism Stage 7 colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 SMED30019097smed_20140614PMID:28072387
Davies et al., 2017		whole organism Stage 6 colorimetric in situ hybridization evidence
blastomereSMED30011862h1SMcG0006253 SMED30019097smed_20140614PMID:28072387
Davies et al., 2017		whole organism Stage 5 colorimetric in situ hybridization evidence
blastomereSMED30011862h1SMcG0006253 SMED30019097smed_20140614PMID:28072387
Davies et al., 2017		whole organism Stage 4 colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 AFD29619.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 8 colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 AFD29619.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 6 colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 AFD29619.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 7 colorimetric in situ hybridization evidence
blastomereSMED30011862h1SMcG0006253 AFD29619.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 5 colorimetric in situ hybridization evidence
blastomereSMED30011862h1SMcG0006253 AFD29619.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 4 colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 JQ425151.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 6 colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 JQ425151.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 7 colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 JQ425151.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 8 colorimetric in situ hybridization evidence
blastomereSMED30011862h1SMcG0006253 JQ425151.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 4 colorimetric in situ hybridization evidence
blastomereSMED30011862h1SMcG0006253 JQ425151.1smed_ncbi_20240424PMID:28072387
Davies et al., 2017		whole organism Stage 5 colorimetric in situ hybridization evidence
sigma neoblastSMED30011862h1SMcG0006253 JQ425151smed_ncbi_20240424PMID:25017721
van Wolfswinkel et al., 2014		FACS sorted cell population asexual adult fluorescence in situ hybridization evidence
sigma neoblastSMED30011862h1SMcG0006253 JQ425151smed_ncbi_20240424PMID:25017721
van Wolfswinkel et al., 2014		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30011862h1SMcG0006253 dd_Smed_v4_7227_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30011862h1SMcG0006253 SmWIOct06_023556GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011862h1SMcG0006253 SMED30019097smed_20140614PMID:22385657
Wagner et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30011862h1SMcG0006253 SMED_11833_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011862h1SMcG0006253 SMED_11833_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011862h1SMcG0006253 SMED_11833_V2_2GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011862h1SMcG0006253 SMED_11833_V2_2GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011862h1SMcG0006253 SMED_17522_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011862h1SMcG0006253 SMED_17522_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011862 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009175:12298..12778 +2387
Homology
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BLAST of SMED30011862 vs. Planmine SMEST
Match: SMESG000078907.1 (SMESG000078907.1)

HSP 1 Score: 71.633 bits (174), Expect = 1.954e-16
Identity = 37/85 (43.53%), Postives = 55/85 (64.71%), Query Frame = -2 
Query:   97 CRAK*QKMKLNISLGQVAAKSSNQ*QESMEVQEASDLFEYWRDYFGYVVVHNFPRVGGHEIELP*RWKLLVXXXXXXXXXKIDLR 351
            C     +M L+++LG+VA +S  Q QE+MEVQ+ S+ FEYW DY G  + H  P+V   ++++P R KL V+M+ +D    IDLR
Sbjct:   81 CADSRDEMSLSLNLGEVAVRSPRQLQETMEVQDVSNSFEYWSDYLGDEIGHTIPQVDSAKLKIPLRRKLPVNMNANDHEIIIDLR 165

HSP 2 Score: 30.8018 bits (68), Expect = 1.954e-16
Identity = 14/28 (50.00%), Postives = 21/28 (75.00%), Query Frame = -1 
Query:  380 ESAVILANASKVLEEASAIVAEKYPDFV 463
            E AV++ANA+ V  E +AI+AE + +FV
Sbjct:   44 EGAVLIANAANVFVELTAIMAEMHLEFV 71
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BLAST of SMED30011862 vs. Planmine SMEST
Match: SMESG000010646.1 (SMESG000010646.1)

HSP 1 Score: 66.6254 bits (161), Expect = 7.343e-15
Identity = 43/91 (47.25%), Postives = 56/91 (61.54%), Query Frame = -2 
Query:  100 STSVTNPCRAK*QKMKLNISLGQVAAKSSNQ*QESMEVQEASDLFEYWRDYFGYVVVHNFPRVGGHEIELP*RWKLLVXXXXXXXXXKIDL 372
            STS  +P      ++KL+I+L Q A  ++ Q Q   E+QE  DL  YW DYFG  V H  P+VGGH   +P R K+LVDMDE+D+   IDL
Sbjct:   11 STSQIHPDPND--ELKLSINLDQTAVGTTKQRQMPTEIQEVYDLSMYWIDYFGDEVTHTVPQVGGHGFRIPQRRKILVDMDEEDRRMIIDL 99
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BLAST of SMED30011862 vs. Planmine SMEST
Match: SMESG000001072.1 (SMESG000001072.1)

HSP 1 Score: 43.8986 bits (102), Expect = 3.112e-9
Identity = 23/53 (43.40%), Postives = 33/53 (62.26%), Query Frame = -1 
Query:  314 RRTESAVILANASKVLEEASAIVAEKYPDFVNQIHQRYKSMPSKVTKNEAEHK 472
            R  E A +LANA+KVLEEA+  VAE++P+FV  + +  +S+       E E K
Sbjct:   47 RGAEGATVLANAAKVLEEAAVRVAEQFPEFVKPVEKSVESLHQISADEEDEMK 99

HSP 2 Score: 34.2686 bits (77), Expect = 3.112e-9
Identity = 21/59 (35.59%), Postives = 32/59 (54.24%), Query Frame = -2 
Query:   88 EVQEASDLFEYWRDYFGYVVVHNFPRVGGHEIELP*RWKLLVXXXXXXXXXKIDLRVRL 264
            E + +S    YW D FG  + H+ P+VG  E + P + K  VD+DE+ +   +D   RL
Sbjct:  116 ETRNSSTSIRYWTDGFGGELSHSVPQVGATEFKFPRKRKFSVDIDEERRDFAVDYFTRL 174
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BLAST of SMED30011862 vs. Planmine SMEST
Match: SMESG000011772.1 (SMESG000011772.1)

HSP 1 Score: 37.3502 bits (85), Expect = 1.600e-6
Identity = 17/28 (60.71%), Postives = 22/28 (78.57%), Query Frame = -1 
Query:  380 ESAVILANASKVLEEASAIVAEKYPDFV 463
            E A +L NA+KVLEEA+  VAE +P+FV
Sbjct:  100 EGATVLPNAAKVLEEAAIRVAEHFPEFV 127

HSP 2 Score: 31.5722 bits (70), Expect = 1.600e-6
Identity = 19/58 (32.76%), Postives = 30/58 (51.72%), Query Frame = -2 
Query:  163 QKMKLNISLGQVAAKSSNQ*QESMEVQEASDLFEYWRDYFGYVVVHNFPRVGGHEIEL 336
            +K +L I L   + +++ Q  E  E + +S    YW D FG    H+ P+VG  E+ L
Sbjct:  150 KKDELKIHLNVSSPETTPQVVE--ETRSSSTSVGYWTDDFGDEFCHSIPQVGTPEMSL 205
The following BLAST results are available for this feature:
BLAST of SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 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 SMED30011862 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000078907.11.954e-1643.53SMESG000078907.1[more]
SMESG000010646.17.343e-1547.25SMESG000010646.1[more]
SMESG000001072.13.112e-943.40SMESG000001072.1[more]
SMESG000011772.11.600e-660.71SMESG000011772.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011862 ID=SMED30011862|Name=SMED30011862|organism=Schmidtea mediterranea sexual|type=transcript|length=481bp
GAAGAAAATAACATAGCAGCCGCTGGATATTGGGGACTTTACGACAGAAA
CTGAGCCATTAGATCGGATACTCGCGATAAATAATTGCAATCTCACCCTC
AGATCGATTTTCTCCATTTTGTCGTCTTCATCCATATCGACGAGTAATTT
CCACCGTCAAGGTAGTTCAATCTCGTGACCACCCACCCGCGGAAAGTTGT
GGACTACCACATATCCGAAGTAGTCCCTCCAATACTCGAAAAGATCTGAT
GCTTCCTGGACCTCCATGGACTCTTGTCACTGGTTGGACGATTTTGCTGC
TACCTGGCCCAGACTTATGTTCAGCTTCATTTTTTGTCACTTTGCTCGGC
ATGGATTTGTAACGCTGGTGGATCTGGTTTACAAAATCTGGGTATTTCTC
GGCCACGATCGCTGATGCTTCCTCCAGCACTTTTGACGCATTGGCGAGGA
TCACTGCACTCTCAGTCCGACGACGTTCACG
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protein sequence of SMED30011862-orf-1

>SMED30011862-orf-1 ID=SMED30011862-orf-1|Name=SMED30011862-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
RERRRTESAVILANASKVLEEASAIVAEKYPDFVNQIHQRYKSMPSKVTK
NEAEHKSGPGSSKIVQPVTRVHGGPGSIRSFRVLEGLLRICGSPQLSAGG
WSRD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 10..32