SMED30024379

Overview
NameSMED30024379
Smed IDSMED30024379
Length (bp)2524
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 SMED30024379 (SMED30024379) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024379 (SMED30024379) 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 SMED30024379 (SMED30024379) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024379 (SMED30024379) 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




SMED30024379

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30024379h1SMcG0014144 dd_Smed_v4_4064_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30024379h1SMcG0014144 dd_Smed_v4_4064_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30024379h1SMcG0014144 dd_Smed_v4_4064_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
SMED30024379 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001439:17608..24801 +12289
Homology
BLAST of SMED30024379 vs. Planmine SMEST
Match: SMESG000024211.1 (SMESG000024211.1)

HSP 1 Score: 882.093 bits (2278), Expect = 0.000e+0
Identity = 533/547 (97.44%), Postives = 535/547 (97.81%), Query Frame = 3
Query:  828 FNLVEDNESISNKLNLTXXXXXXXXXXXXXXXXXTXXXXXXXXXXXXXXXXXXXXXX-XTMVIDYXXXXXXXXXXXXXAPYGNHCDDDELETICSKIKTENKDLKQEIYELKQKLNDLSIMSATIGNLKKENEIYLKKQVDLERTCSAIQKELTNSLQKMNSAETRLVRMNTERNQQISYFENEIHKCNNKISILEADLRSKTTDNENLKMSVEQIRHLVSDKEQLLQNQNTELSFLNEQYYKTRKDYQEIELSANNITMKYKDLENQNQKLLDENQKMKYQMDSVKKENHKELEKFKMQIQNKERDQNSLISSLQYQIDEFQKEKQLSMFNSELDELRQENEKLKNTYAANRNNSCPSTPAGFELIETDKIKQITSKIIEGNRKLQEKCDQYNSLLSEKSDXXXXXXXXXXXXXXDYSKLNKNLEEHLNEIVNLRTCIEKLQFDLSKNCENNFDDMKMELERKCETLRKTEEILTKLQVSVEDEEMRWNDLLSERIQDXXXXXXXXXXXXXVISNQNKKISELTSMLQSTNYPQMDSTLNGSLSVE 2465
            FN VEDNESISNKLNLTKSKKIPNKKPKNCPSNSTESSLGNEKLLSSS    +   L ET+VIDYKEE KNPEIINNNAPYGNHCDDDELETICSKIKTENKDLKQEIYELKQKLNDLSIMSATIGNLKKENEIYLKKQVDLERTCSAIQKELTNSLQKMNSAETRLVRMNTERNQQISYFENEIHKCNNKISILEADLRSKTTDNENLKMSVEQIRHLVSDKEQLLQNQNTELSFLNEQYYKTRKDYQEIELSANNITMKYKDLENQNQKLLDENQKMKYQMDSVKKENHKELEKFKMQIQNKERDQNSLISSLQYQIDEFQKEKQLSMFNSELDELRQENEKLKN YAANRNNSCPSTPAGFELIETDKIKQITSKIIEGNRKLQEKCDQYNSLLSEKSDKENLLLEKNAKLE DYSKLNKNLEEHLNEIVNLRTCIEKLQFDLSKNCENNFDDMKMELERKCETLRKTEEILTKLQVSVEDEEMRWNDLLSERIQDNEKLENELAEKNLVISNQNKKISELTSMLQSTNYPQMDSTLNGSLSVE
Sbjct:  208 FNCVEDNESISNKLNLTKSKKIPNKKPKNCPSNSTESSLGNEKLLSSSSLELEDKSLLETIVIDYKEESKNPEIINNNAPYGNHCDDDELETICSKIKTENKDLKQEIYELKQKLNDLSIMSATIGNLKKENEIYLKKQVDLERTCSAIQKELTNSLQKMNSAETRLVRMNTERNQQISYFENEIHKCNNKISILEADLRSKTTDNENLKMSVEQIRHLVSDKEQLLQNQNTELSFLNEQYYKTRKDYQEIELSANNITMKYKDLENQNQKLLDENQKMKYQMDSVKKENHKELEKFKMQIQNKERDQNSLISSLQYQIDEFQKEKQLSMFNSELDELRQENEKLKNMYAANRNNSCPSTPAGFELIETDKIKQITSKIIEGNRKLQEKCDQYNSLLSEKSDKENLLLEKNAKLEKDYSKLNKNLEEHLNEIVNLRTCIEKLQFDLSKNCENNFDDMKMELERKCETLRKTEEILTKLQVSVEDEEMRWNDLLSERIQDNEKLENELAEKNLVISNQNKKISELTSMLQSTNYPQMDSTLNGSLSVE 754          
The following BLAST results are available for this feature:
BLAST of SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 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 SMED30024379 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000024211.10.000e+097.44SMESG000024211.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024379 ID=SMED30024379|Name=SMED30024379|organism=Schmidtea mediterranea sexual|type=transcript|length=2524bp
TGAAATTGTAATCCAAAACTGCCCTGGAACCTTTTACACAACCTAGTATA
TTCAGGGATATTTGGCTTGTGACATGGTTCCCGTTTGTCAAAGAACCCTG
AATAATTCATGCTGGATTAAATACTAATCAAAATTGAATAATTGTTATTT
TCGATCCGTTTTAATTTGCAAGTGATATAAAATAAAATAAATGAAATACA
ATAATTTATCGGCACATAAACATTTGGATGGTGTGTTCAACATATTTGTT
TTTGTCTTGGATGTGGCGAAACTTTCAGCTTATCCTCGTGAAAATATACT
AATCCTAGAATCCATATACAAATATAATCTCGTACATTTGTTGAGATAAA
ATAACTCCATTCTTTACGCCAGTTTTATTGGTGTCATTTAAAGCCTCAAA
GCCAAATCACATAGCATACTTAATAATGAGCAGTTTACCCACTAACTTTA
TTTTCCTGGTTTTTCATCATTAAACTACTTTTGTTTCATTATTTATAACA
TTTTTTAAAGCAATCAAATTAAAGTGAATAATACGTTGCCAGAAATGTTA
TGTTAAAAATGATGAAAACTTTTTTTATAATAATTTATTTTATTTATTAA
TTCAGAAGGATCAAATCGAATTTTGAAAACTAAGGTCATAAAAATAATTC
TAATTCTATGATTTGTAATCTCTATTGTAAATTGTTTAGTTTTTCATTTT
GTTTATGATTATGTTTCAAGTTATTCAAAGTCCAATATGTTTGCTAAAAT
TATTTTTTGTACTACTTTATATTTAATATTTATTTAAACTAAACTAACCA
AATTTGCCACCTGATGATGGATTTTTATTTAATTTAGTTGAAGATAATGA
AAGTATCTCGAATAAATTAAACTTAACCAAAAGTAAGAAAATACCCAATA
AAAAACCGAAAAATTGTCCATCTAATTCAACTGAATCTAGTTTGGGCAAT
GAAAAATTGCTTTCTTCGTCATTAGAGCTGGAAGACAAAAGTCTTTTGGA
AACTATGGTTATAGACTATAAAGAAGAACCAAAAAATCCCGAAATAATCA
ATAATAATGCTCCTTATGGAAATCATTGCGATGATGATGAATTGGAAACG
ATTTGCAGTAAAATTAAAACAGAAAATAAGGATTTGAAACAGGAAATATA
TGAATTGAAACAGAAATTAAACGATCTATCGATTATGTCGGCTACAATTG
GAAACCTTAAAAAAGAAAACGAAATATATCTGAAAAAACAAGTAGATCTT
GAAAGAACATGTTCAGCAATACAAAAAGAATTAACAAACAGCCTACAAAA
GATGAATTCAGCTGAAACACGTCTTGTCAGAATGAATACTGAGAGAAATC
AACAGATTTCATATTTTGAGAATGAAATCCACAAGTGTAACAATAAAATA
TCAATACTAGAAGCAGATCTGCGTTCCAAAACCACGGATAATGAGAACCT
GAAAATGAGCGTGGAACAAATTAGACATTTAGTATCTGACAAAGAACAAC
TATTGCAGAATCAAAATACTGAATTATCTTTTTTAAACGAACAATATTAT
AAAACTCGCAAAGATTATCAGGAAATTGAACTTTCAGCAAATAATATCAC
AATGAAATATAAGGACCTTGAAAATCAAAACCAAAAATTACTAGATGAAA
ACCAAAAAATGAAATATCAGATGGATTCAGTTAAAAAGGAAAACCATAAA
GAATTAGAAAAATTCAAAATGCAAATTCAAAATAAAGAAAGAGATCAAAA
TTCTTTGATTTCTAGTTTGCAATATCAAATTGATGAATTCCAAAAAGAGA
AGCAATTATCTATGTTTAATTCGGAACTAGATGAACTCAGACAAGAAAAT
GAGAAGCTGAAAAATACGTATGCTGCTAATCGTAACAATTCATGTCCTTC
AACTCCCGCCGGATTTGAATTGATTGAAACTGACAAAATTAAACAAATAA
CATCAAAAATAATCGAGGGAAATCGAAAATTGCAAGAAAAATGTGACCAA
TACAATTCATTGCTATCTGAAAAAAGTGACAAAGAAAATTTATTGCTGGA
AAAAAATGCAAAATTGGAAAATGATTACTCAAAACTAAATAAAAACCTAG
AAGAACATTTAAATGAAATAGTTAATCTGAGAACTTGCATAGAAAAATTA
CAATTCGATCTTTCAAAAAATTGTGAAAATAATTTTGATGATATGAAAAT
GGAATTAGAAAGAAAATGTGAAACATTGAGGAAAACCGAAGAAATTCTTA
CTAAATTACAAGTTTCTGTTGAAGATGAAGAGATGAGATGGAATGATTTG
CTTAGTGAAAGAATTCAGGACAATGAAAAGTTAGAAAATGAGCTAGCAGA
AAAAAATTTGGTAATATCGAATCAAAACAAGAAAATCTCTGAACTCACAT
CTATGCTACAGTCGACCAATTATCCTCAAATGGACTCGACATTAAATGGT
TCTCTCTCTGTAGAATAAAATAAAGTTTAAATAAAAATTATTTATAATAA
TATTAATATTGATACTGATAATAA
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protein sequence of SMED30024379-orf-1

>SMED30024379-orf-1 ID=SMED30024379-orf-1|Name=SMED30024379-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=488bp
MVIDYKEEPKNPEIINNNAPYGNHCDDDELETICSKIKTENKDLKQEIYE
LKQKLNDLSIMSATIGNLKKENEIYLKKQVDLERTCSAIQKELTNSLQKM
NSAETRLVRMNTERNQQISYFENEIHKCNNKISILEADLRSKTTDNENLK
MSVEQIRHLVSDKEQLLQNQNTELSFLNEQYYKTRKDYQEIELSANNITM
KYKDLENQNQKLLDENQKMKYQMDSVKKENHKELEKFKMQIQNKERDQNS
LISSLQYQIDEFQKEKQLSMFNSELDELRQENEKLKNTYAANRNNSCPST
PAGFELIETDKIKQITSKIIEGNRKLQEKCDQYNSLLSEKSDKENLLLEK
NAKLENDYSKLNKNLEEHLNEIVNLRTCIEKLQFDLSKNCENNFDDMKME
LERKCETLRKTEEILTKLQVSVEDEEMRWNDLLSERIQDNEKLENELAEK
NLVISNQNKKISELTSMLQSTNYPQMDSTLNGSLSVE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
Vocabulary: biological process
TermDefinition
GO:0006355regulation of transcription, DNA-templated
Vocabulary: molecular function
TermDefinition
GO:0003700transcription factor activity, sequence-specific DNA binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 338..368
NoneNo IPR availableCOILSCoilCoilcoord: 263..318
NoneNo IPR availableCOILSCoilCoilcoord: 128..187
NoneNo IPR availableCOILSCoilCoilcoord: 100..120
NoneNo IPR availableCOILSCoilCoilcoord: 373..400
NoneNo IPR availableCOILSCoilCoilcoord: 208..235