SMED30019934

Overview
NameSMED30019934
Smed IDSMED30019934
Length (bp)1176
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 SMED30019934 (SMED30019934) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30019934 (SMED30019934) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30019934 (SMED30019934) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30019934 (SMED30019934) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30019934

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30019934h1SMcG0014655 Contig50799uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30019934h1SMcG0014655 Contig50799newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30019934h1SMcG0014655 dd_Smed_v4_815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30019934h1SMcG0014655 dd_Smed_v4_815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30019934h1SMcG0014655 dd_Smed_v4_815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30019934h1SMcG0014655 dd_Smed_v4_815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30019934h1SMcG0014655 dd_Smed_v4_815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30019934h1SMcG0014655 dd_Smed_v4_815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30019934h1SMcG0014655 dd_Smed_v4_815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30019934h1SMcG0014655 dd_Smed_v6_815_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cholinergic neuronSMED30019934h1SMcG0014655 dd_Smed_v6_815_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30019934h1SMcG0014655 dd_Smed_v6_815_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30019934h1SMcG0014655 dd_Smed_v6_815_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30019934h1SMcG0014655 dd_Smed_v6_815_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30019934 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000609:35807..37028 -4846
Homology
[Close]
BLAST of SMED30019934 vs. Planmine SMEST
Match: SMESG000009290.1 (SMESG000009290.1)

HSP 1 Score: 132.88 bits (333), Expect = 4.512e-37
Identity = 111/112 (99.11%), Postives = 111/112 (99.11%), Query Frame = 2 
Query:  236 MGNKSGKFEVTKTDKEVKENAEAPVDAEHIEAVKEEKVESIPEAEPKENGDAAESXXXXXXXXXXXXXAPXXXXXXXXXXXXXXXXXXXXXXXGVFGWLKKISFRKEKKTKS 571
            MGNKSGKFEVTKTDKEVKENAEA VDAEHIEAVKEEKVESIPEAEPKENGDAAESKEVVENTTEENKEAPETAAVIEEEKKTETVETNEPKKKGVFGWLKKISFRKEKKTKS
Sbjct:    1 MGNKSGKFEVTKTDKEVKENAEAQVDAEHIEAVKEEKVESIPEAEPKENGDAAESKEVVENTTEENKEAPETAAVIEEEKKTETVETNEPKKKGVFGWLKKISFRKEKKTKS 112
The following BLAST results are available for this feature:
BLAST of SMED30019934 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019934 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000009290.14.512e-3799.11SMESG000009290.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019934 ID=SMED30019934|Name=SMED30019934|organism=Schmidtea mediterranea sexual|type=transcript|length=1176bp
TTGGTTGATTCAAAATCGATCATGCATTCTCGCTCGAGTCTACATACAAT
CCAATCCAGTATTCTTCTCTCTCAGGCTAACCACTGCAGTATCAAACGAG
ATGACACACTCATTCAATAACTGTTCAGCCAGCTAACCAGATATTATTCA
TACTTATTGTTCAGTTCATCATTTACTCCAGTTTTCACGAACGTAAATTA
ATTCTTCAAAAACAAAAAACCAAAACCAATTCGAAATGGGAAATAAATCT
GGAAAATTCGAAGTCACTAAAACCGACAAAGAAGTCAAAGAAAATGCTGA
AGCCCCAGTTGATGCCGAACACATTGAAGCTGTCAAAGAAGAAAAAGTAG
AATCTATACCAGAAGCAGAACCTAAGGAAAACGGTGATGCTGCCGAATCA
AAAGAAGTTGTTGAGAATACCACCGAAGAAAACAAAGAAGCCCCAGAAAC
AGCAGCAGTTATCGAAGAAGAAAAGAAAACTGAAACCGTTGAAACGAATG
AACCAAAAAAGAAAGGAGTATTTGGATGGTTGAAGAAAATATCATTTAGA
AAAGAAAAGAAAACCAAATCCAATACTGATGAAGCCAATGAAACTGAGGA
AAACAAAGAAATTAAAACCGAGGAAGCTAAAGTTGAAGAAAAACACGAAG
AAGCTACAGAAGAAAAAGTCGAAACAGTCGAAGAGACAAAACCACAAGAA
AACAACACTACTGAGGAAGAGAAGAAAGACGAAGAAGCCAAACCATCAGA
AGAGCAAAATTAAAACAAAATCTTCAAATCAAACGTCAGAAATATTAAAT
TCATTATTTTCCCTGAATTTGAAAAGCGATTGTTTTCATTTTTTTTTGAA
AAAACAATATATGATTAATTTTTTTTTAACCTAGTGTTTATACTTTGAAT
ACTATTATATATCAAACATTTCATACAATTACTCTTCGATAAAAATTGTT
CTTTATTATCAAAATTTTGACGACAAACACCTGATAATAATAGTTATTAT
TATTAAATGATTTGAAAATTTTTTTTGTATATATTTCTGATAATATTATT
CGAATACGTGCTGATGATAATATTTGTGATATTTATAGAAAATTGTTGAT
ACTACTAATATTCTGTAGGCGTTATACTATTTGTTCTATTGTTGGTTTTT
CTTTCAAATGTTTTTTTTGATTTAAG
back to top

protein sequence of SMED30019934-orf-1

>SMED30019934-orf-1 ID=SMED30019934-orf-1|Name=SMED30019934-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=176bp
MGNKSGKFEVTKTDKEVKENAEAPVDAEHIEAVKEEKVESIPEAEPKENG
DAAESKEVVENTTEENKEAPETAAVIEEEKKTETVETNEPKKKGVFGWLK
KISFRKEKKTKSNTDEANETEENKEIKTEEAKVEEKHEEATEEKVETVEE
TKPQENNTTEEEKKDEEAKPSEEQN*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000463cholinergic neuron
PLANA:0000478pharynx musculature
PLANA:0003116parenchymal cell
PLANA:0007528glial cell
Vocabulary: INTERPRO
TermDefinition
IPR011528NERD
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 117..143
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 8..175
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..175