SMED30026678

Overview
NameSMED30026678
Smed IDSMED30026678
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 SMED30026678 (SMED30026678) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026678 (SMED30026678) 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 SMED30026678 (SMED30026678) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026678 (SMED30026678) 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



SMED30026678

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
head regionSMED30026678 SmedASXL_079571SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30026678 dd_Smed_v4_3577_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026678 dd_Smed_v4_3577_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30026678 dd_Smed_v4_3577_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30026678 dd_Smed_v4_3577_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30026678 dd_Smed_v4_3577_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30026678 dd_Smed_v4_3577_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30026678 dd_Smed_v4_3577_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30026678 dd_Smed_v4_3577_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026678 Contig50961newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026678 Contig50961uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30026678 dd_Smed_v6_3577_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
neuronSMED30026678 dd_Smed_v6_3577_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cholinergic neuronSMED30026678 dd_Smed_v6_3577_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
SMED30026678 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001411:53007..53482 +2371
Homology
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BLAST of SMED30026678 vs. TrEMBL
Match: A0A267FEU5 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig019061g1 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 6.313e-9
Identity = 27/74 (36.49%), Postives = 46/74 (62.16%), Query Frame = 3 
Query:   87 SIILFIICIHS-VYSVIYEEAQKDRNRYIRYDDSTFNTFLHVGLALLLSYSILIFLWCMINLVFKLHGQKRISR 305
            +++L +  +HS V SV  +E + +  +YI YD   FN ++H+ ++L + Y+ILIF+W  + L  KL G+ R  R
Sbjct:    6 TVVLILAALHSPVRSVTLQEGKSNPQKYIYYDTDEFNPWIHLAISLPILYAILIFIWSGVTLYMKLSGKSRQRR 79
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BLAST of SMED30026678 vs. TrEMBL
Match: A0A0R3SMB4 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS6077 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 5.961e-7
Identity = 26/59 (44.07%), Postives = 36/59 (61.02%), Query Frame = 3 
Query:   69 MDFFFKSI-ILFIICIHSVYSVIYEEAQKDRNRYIRYDDSTFNTFLHVGLALLLSYSIL 242
            M +   SI ILFI   H   ++  EE   D+ +YI YD S+FN  +H GLALL+++ IL
Sbjct:    1 MSYILPSICILFIALTHMASAITLEEGMADKTKYIFYDTSSFNPGIHAGLALLITFGIL 59
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BLAST of SMED30026678 vs. TrEMBL
Match: A0A448X4N9 (Uncharacterized protein OS=Protopolystoma xenopodis OX=117903 GN=PXEA_LOCUS21400 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 6.690e-7
Identity = 28/61 (45.90%), Postives = 41/61 (67.21%), Query Frame = 3 
Query:  123 YSVIYEEAQKDRNRYIRYDDSTFNTFLHVGLALLLSYSILIFLWCMINLVFKLHGQKRISR 305
            ++V  EEA+K+  +YI Y+++ FN  +HVGLA+L++Y  L FL   I +V KL  QKR  R
Sbjct:   30 WAVTLEEARKNPKQYILYEEAPFNIGMHVGLAMLVTYGALTFLVIFIAVVSKLV-QKRSKR 89
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BLAST of SMED30026678 vs. TrEMBL
Match: A0A267DR65 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig017648g1 PE=4 SV=1)

HSP 1 Score: 53.5286 bits (127), Expect = 1.418e-6
Identity = 23/63 (36.51%), Postives = 37/63 (58.73%), Query Frame = 3 
Query:  117 SVYSVIYEEAQKDRNRYIRYDDSTFNTFLHVGLALLLSYSILIFLWCMINLVFKLHGQKRISR 305
             V  V  +E + +  +YI YD   FN ++H+ ++L + Y+ILIF+W  + L  KL G+ R  R
Sbjct:   18 PVRGVTLQEGKSNPQKYIYYDTDEFNPWIHLAISLPILYAILIFIWSGVTLYMKLSGKSRQRR 80
[Close]
BLAST of SMED30026678 vs. TrEMBL
Match: A0A0R3U4Q5 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS1643 PE=4 SV=1)

HSP 1 Score: 55.0694 bits (131), Expect = 2.289e-6
Identity = 27/84 (32.14%), Postives = 46/84 (54.76%), Query Frame = 3 
Query:   57 KEFVMDFFFKSIILFIICI-HSVYSVIYEEAQKDRNRYIRYDDSTFNTFLHVGLALLLSYSILIFLWCMINLVFKLHGQKRISR 305
            K  +++  F  II   + I  + Y++  +E   D+ +YI YD S FN  +H GLALL++Y IL      + ++ K+  ++R  R
Sbjct:   82 KAIILNMSFLGIIAVALAICQTAYAITLQEGMADKEKYIFYDTSPFNVGMHAGLALLITYGILGTFTPTVMIITKILEKRRQRR 165
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BLAST of SMED30026678 vs. Planmine SMEST
Match: SMESG000035183.1 (SMESG000035183.1)

HSP 1 Score: 68.9366 bits (167), Expect = 7.456e-16
Identity = 28/68 (41.18%), Postives = 47/68 (69.12%), Query Frame = 3 
Query:  117 SVYSVIYEEAQKDRNRYIRYDDSTFNTFLHVGLALLLSYSILIFLWCMINLVFKLHGQKRISRTYD*H 320
             V SV  E+ +++   YI+YD S  N  LH+GL++L++++IL  +WC++N +FKL  + R +RTY+ H
Sbjct:   23 KVQSVTLEDGKQNPGLYIKYDTSEMNLGLHIGLSILITFAILTIIWCIVNAIFKLQKKPRRTRTYESH 90
[Close]
BLAST of SMED30026678 vs. Planmine SMEST
Match: SMESG000022725.1 (SMESG000022725.1)

HSP 1 Score: 53.5286 bits (127), Expect = 3.286e-10
Identity = 23/65 (35.38%), Postives = 39/65 (60.00%), Query Frame = 3 
Query:  120 VYSVIYEEAQKDRNRYIRYDDSTFNTFLHVGLALLLSYSILIFLWCMINLVFKLHGQKRISRTYD 314
            V  V    A K+ + YI+YD + F  + H+G++L + Y+IL  +W M+NL+FK+   K++    D
Sbjct:    4 VKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIWSMVNLIFKIRELKKVGTELD 68
The following BLAST results are available for this feature:
BLAST of SMED30026678 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 SMED30026678 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 SMED30026678 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 SMED30026678 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 SMED30026678 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 SMED30026678 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 SMED30026678 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 SMED30026678 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267FEU56.313e-936.49Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A0R3SMB45.961e-744.07Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A448X4N96.690e-745.90Uncharacterized protein OS=Protopolystoma xenopodi... [more]
A0A267DR651.418e-636.51Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A0R3U4Q52.289e-632.14Uncharacterized protein OS=Mesocestoides corti OX=... [more]
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BLAST of SMED30026678 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 SMED30026678 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 SMED30026678 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 SMED30026678 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 SMED30026678 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 SMED30026678 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000035183.17.456e-1641.18SMESG000035183.1[more]
SMESG000022725.13.286e-1035.38SMESG000022725.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026678 ID=SMED30026678|Name=SMED30026678|organism=Schmidtea mediterranea sexual|type=transcript|length=481bp
GGGGTACAATTTCATTTGTTCACAATTTTTACATTTCATTTTGACATTTT
ATTATTAAGGAATTTGTAATGGATTTTTTTTTCAAATCTATAATACTATT
TATTATTTGTATACATTCTGTATACAGTGTGATTTACGAAGAAGCTCAAA
AAGATCGGAATAGATATATTCGATATGATGATTCAACTTTCAATACGTTT
TTACATGTCGGATTGGCCTTATTACTTTCATATAGCATTTTGATATTTCT
TTGGTGTATGATAAACTTGGTTTTCAAACTACATGGACAGAAAAGAATTT
CTAGAACATATGATTAACATTTTTTTACATTTTCAGTACAATAGGATTTC
AACAAAAACAGTATGAGTTTAGATTAAATTAGTGTTTTTAGATAAAAATG
TATATAGTTTTTGTGTTACAATCTGTTAAATTTATGTTATTATTTCGTCA
ATATATGTAATATTAAATATATATTTAATTC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
PLANA:0000463cholinergic neuron
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-TMSignalP-TMcoord: 1..20
score: 0.589
NoneNo IPR availableTMHMMTMhelixcoord: 43..65
NoneNo IPR availableTMHMMTMhelixcoord: 4..23