SMED30014404

Overview
NameSMED30014404
Smed IDSMED30014404
Length (bp)1082
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30014404 (SMED30014404) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014404 (SMED30014404) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30014404

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30014404h1SMcG0022501 SmedASXL_012970SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30014404h1SMcG0022501 SmedASXL_076914SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30014404h1SMcG0022501 SmedASXL_080656SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
protonephridiaSMED30014404h1SMcG0022501 dd_Smed_v4_14091_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30014404 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000843:61577..63580 +5213
Homology
[Close]
BLAST of SMED30014404 vs. Planmine SMEST
Match: SMESG000009905.1 (SMESG000009905.1)

HSP 1 Score: 474.552 bits (1220), Expect = 1.795e-169
Identity = 297/301 (98.67%), Postives = 298/301 (99.00%), Query Frame = 1 
Query:  145 MVSVFLIVICLVTFSLAENVEDGVYKIFSLCLDGYCAKKEFTVSNMDSSVARGLEMTQQFTDEFKWIITSYIDNIFIIQYKDGIENGDTFTMVLGSKADGDFQLYKELDIDHVLFWKWIKLDSEYSLEVNPISQFNQGKVLCTEKVLLIEYKYCDEILIFEKIPNPRTREQKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPELVTPAVMKCEKCVKNQRKIHRXXXXXXXXXXXXXXXXXXXXXXXGIWKLDVKLAEKRKPSKDHGNNSRSPFDAETKIFVMGPL 1047
            MVSV LI+ICLVTFSLAENVEDGVYKIFSLCLDGYCAKKEFTVSNMDSSVARGLEMTQQFTDEFKWIITSYIDNIFIIQYKDGIENGDTFTMVLGSKADGDFQLYKELDIDHVLFWKWIKLDSEYSLEVNPISQFNQGKVLCTEKVLLIEYKYCDEILIFEKIPNPRTREQKTTTTTTTTTTTTTATTTTTSAT TTTTMIPTTTTEATTTSPP TPELVTPAVMKCEKCVKNQRKIHRTLIITIIISFVIFIILTVLIVWFGIWKLDVKLAEKRKPSKDHGNNSRSPFDAETKIFVMGPL
Sbjct:    1 MVSVLLIIICLVTFSLAENVEDGVYKIFSLCLDGYCAKKEFTVSNMDSSVARGLEMTQQFTDEFKWIITSYIDNIFIIQYKDGIENGDTFTMVLGSKADGDFQLYKELDIDHVLFWKWIKLDSEYSLEVNPISQFNQGKVLCTEKVLLIEYKYCDEILIFEKIPNPRTREQKTTTTTTTTTTTTTATTTTTSATATTTTMIPTTTTEATTTSPPITPELVTPAVMKCEKCVKNQRKIHRTLIITIIISFVIFIILTVLIVWFGIWKLDVKLAEKRKPSKDHGNNSRSPFDAETKIFVMGPL 301
The following BLAST results are available for this feature:
BLAST of SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 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 SMED30014404 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000009905.11.795e-16998.67SMESG000009905.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014404 ID=SMED30014404|Name=SMED30014404|organism=Schmidtea mediterranea sexual|type=transcript|length=1082bp
AAAAAAAGTCCTTATAATATTTTGTGAAGCTTTGTTACAAAGGAATTTAT
ATTCCAAAGATCTTTGATAATCTGTAGCAACGGTGGACCTAACTGAACTA
TTTCATTTGACCTGAACAATCTCAGAATTTTGTTTATTCATCTAATGGTC
TCAGTGTTTCTGATCGTCATTTGTTTGGTCACTTTCTCTCTAGCAGAAAA
TGTCGAAGATGGAGTTTATAAGATCTTTTCTCTCTGCTTGGACGGATATT
GTGCAAAAAAAGAATTCACGGTTTCAAATATGGATAGTTCTGTAGCAAGA
GGTTTAGAGATGACCCAACAATTCACAGACGAGTTCAAATGGATTATTAC
AAGTTACATTGACAACATTTTCATCATTCAATATAAAGATGGCATTGAAA
ACGGGGACACCTTTACAATGGTTCTGGGATCAAAAGCCGATGGTGATTTT
CAGTTATACAAAGAATTAGATATTGACCATGTCTTGTTTTGGAAATGGAT
AAAACTCGATAGTGAATATAGCTTAGAAGTCAATCCAATCTCCCAATTTA
ACCAAGGAAAAGTTTTATGTACAGAAAAGGTTTTACTGATTGAATATAAA
TATTGTGATGAGATACTAATTTTTGAAAAAATCCCTAACCCTAGAACACG
AGAACAAAAAACTACAACGACTACGACAACGACAACGACGACCACAACTG
CAACCACTACTACAACATCGGCAACTACTACCACAACAACAATGATTCCT
ACAACCACAACAGAGGCTACAACTACTTCCCCGCCAACAACTCCCGAGTT
GGTAACTCCGGCTGTTATGAAATGTGAAAAATGTGTCAAAAACCAAAGGA
AAATCCACAGAACTCTAATAATAACTATAATCATCTCATTTGTTATTTTC
ATCATTCTCACAGTTCTGATTGTTTGGTTCGGTATTTGGAAGCTGGATGT
CAAACTAGCTGAAAAAAGAAAGCCTTCCAAAGATCATGGAAATAATTCTC
GAAGCCCCTTTGATGCAGAAACAAAAATATTTGTAATGGGACCTTTGCAA
AGTCGAATATGAGTTCGACATTTAGAGAAGAC
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protein sequence of SMED30014404-orf-1

>SMED30014404-orf-1 ID=SMED30014404-orf-1|Name=SMED30014404-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=306bp
MVSVFLIVICLVTFSLAENVEDGVYKIFSLCLDGYCAKKEFTVSNMDSSV
ARGLEMTQQFTDEFKWIITSYIDNIFIIQYKDGIENGDTFTMVLGSKADG
DFQLYKELDIDHVLFWKWIKLDSEYSLEVNPISQFNQGKVLCTEKVLLIE
YKYCDEILIFEKIPNPRTREQKTTTTTTTTTTTTTATTTTTSATTTTTTM
IPTTTTEATTTSPPTTPELVTPAVMKCEKCVKNQRKIHRTLIITIIISFV
IFIILTVLIVWFGIWKLDVKLAEKRKPSKDHGNNSRSPFDAETKIFVMGP
LQSRI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000418head