X1.D.D8.3

Overview
NameX1.D.D8.3 (AHD24757.1)
Smed IDSMED30026803
Length (bp)651
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 X1.D.D8.3 (SMED30026803) t-SNE clustered cells

Violin plots show distribution of expression levels for X1.D.D8.3 (SMED30026803) 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 X1.D.D8.3 (SMED30026803) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for X1.D.D8.3 (SMED30026803) 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



SMED30026803

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



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30026803h1SMcG0017434 SmedASXL_005659SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30026803h1SMcG0017434 SmedASXL_005659SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30026803h1SMcG0001370 Contig4928uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026803h1SMcG0001370 Contig4928newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026803h1SMcG0017434 Contig4928uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026803h1SMcG0017434 Contig4928newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026803h1SMcG0017436 Contig42746uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026803h1SMcG0017436 Contig42746newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026803h1SMcG0017434 Contig42746uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026803h1SMcG0017434 Contig42746newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30026803h1SMcG0017434 dd_Smed_v4_8540_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30026803h1SMcG0017434 dd_Smed_v4_8540_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30026803h1SMcG0017434 dd_Smed_v4_8540_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30026803h1SMcG0017434 dd_Smed_v4_8540_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30026803h1SMcG0017434 dd_Smed_v4_8540_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026803h1SMcG0017434 dd_Smed_v4_8540_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30026803h1SMcG0017434 dd_Smed_v4_8540_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30026803h1SMcG0017434 dd_Smed_v4_8540_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30026803h1SMcG0017434 dd_Smed_v6_8540_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
Homology
[Close]
BLAST of X1.D.D8.3 vs. TrEMBL
Match: V9XQR7 (X1.D.D8.3 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 281.567 bits (719), Expect = 2.136e-94
Identity = 141/142 (99.30%), Postives = 141/142 (99.30%), Query Frame = 1 
Query:  157 MKIFSALLLLIFGAIFSEFKQLKKNEKIILKKCDKRYSNVDRKCDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNIGCSLFS 582
            MKIFSALLLLIFGAIFSEFKQLKKNEKIILKKCDKRYSNVDR CDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNIGCSLFS
Sbjct:    1 MKIFSALLLLIFGAIFSEFKQLKKNEKIILKKCDKRYSNVDRNCDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNIGCSLFS 142
[Close]
BLAST of X1.D.D8.3 vs. Planmine SMEST
Match: SMESG000053883.1 (SMESG000053883.1)

HSP 1 Score: 281.567 bits (719), Expect = 4.230e-98
Identity = 141/142 (99.30%), Postives = 142/142 (100.00%), Query Frame = 1 
Query:  157 MKIFSALLLLIFGAIFSEFKQLKKNEKIILKKCDKRYSNVDRKCDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNIGCSLFS 582
            MKIFSALLLLIFGAIFSEFKQLKKN+KIILKKCDKRYSNVDRKCDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNIGCSLFS
Sbjct:    1 MKIFSALLLLIFGAIFSEFKQLKKNQKIILKKCDKRYSNVDRKCDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNIGCSLFS 142
[Close]
BLAST of X1.D.D8.3 vs. Planmine SMEST
Match: SMESG000024881.1 (SMESG000024881.1)

HSP 1 Score: 46.2098 bits (108), Expect = 2.047e-6
Identity = 24/102 (23.53%), Postives = 50/102 (49.02%), Query Frame = 1 
Query:  250 KCDKRYSNVDRKCDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVY 555
            +C+  Y  +D+ CD  Y+A+ + C   +  +++   K     N++CQ   T+    + +   +Q + D+ KL+  C      +DK C+    ++D+ C  +Y
Sbjct:   41 ECEDEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKCQETPTKAGRKVVRDLEKQIFGDYDKLDKTCDPQYAALDKECLEQYQKLDKHCLPLY 142
[Close]
BLAST of X1.D.D8.3 vs. Planmine SMEST
Match: SMESG000024478.1 (SMESG000024478.1)

HSP 1 Score: 45.4394 bits (106), Expect = 2.701e-6
Identity = 28/108 (25.93%), Postives = 53/108 (49.07%), Query Frame = 1 
Query:  241 ILKKCDKRYSNVDRKCDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNI 564
            I  +CD +Y  +DR+CD +Y++I   C   +  LS            RC++ +TE C+           + +  L++ C ++L  + + C    +RVD  C ++YN++
Sbjct:   25 IDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSG-----------RCRVKLTEDCI-----------KRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 110
[Close]
BLAST of X1.D.D8.3 vs. Planmine SMEST
Match: SMESG000024473.1 (SMESG000024473.1)

HSP 1 Score: 45.4394 bits (106), Expect = 2.701e-6
Identity = 28/108 (25.93%), Postives = 53/108 (49.07%), Query Frame = 1 
Query:  241 ILKKCDKRYSNVDRKCDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNI 564
            I  +CD +Y  +DR+CD +Y++I   C   +  LS            RC++ +TE C+           + +  L++ C ++L  + + C    +RVD  C ++YN++
Sbjct:   25 IDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSG-----------RCRVKLTEDCI-----------KRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 110
[Close]
BLAST of X1.D.D8.3 vs. Planmine SMEST
Match: SMESG000024478.1 (SMESG000024478.1)

HSP 1 Score: 45.4394 bits (106), Expect = 2.748e-6
Identity = 28/108 (25.93%), Postives = 53/108 (49.07%), Query Frame = 1 
Query:  241 ILKKCDKRYSNVDRKCDVAYDAIRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDFLKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNI 564
            I  +CD +Y  +DR+CD +Y++I   C   +  LS            RC++ +TE C+           + +  L++ C ++L  + + C    +RVD  C ++YN++
Sbjct:   36 IDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSG-----------RCRVKLTEDCI-----------KRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALYNHL 121
The following BLAST results are available for this feature:
BLAST of X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XQR72.136e-9499.30X1.D.D8.3 OS=Schmidtea mediterranea OX=79327 PE=2 ... [more]
back to top
BLAST of X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 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 X1.D.D8.3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000053883.14.230e-9899.30SMESG000053883.1[more]
SMESG000024881.12.047e-623.53SMESG000024881.1[more]
SMESG000024478.12.701e-625.93SMESG000024478.1[more]
SMESG000024473.12.701e-625.93SMESG000024473.1[more]
SMESG000024478.12.748e-625.93SMESG000024478.1[more]
back to top
Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30026803
GenBankAHD24757.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026803 ID=SMED30026803|Name=X1.D.D8.3|organism=Schmidtea mediterranea sexual|type=transcript|length=651bp
GTTTTTCAAAAAGTTTGCTAAAACAGAATCATTACGCATTACCATGAGTT
GGCGGTGAATTGCAAATGAGTAATGACGTGAAAGGTAAGAAATATGACGT
CATCTCGATTCTGATTGGACAAAATTAATCAATCTCAAATTACTGATTCA
TACTCGATGAAGATCTTTTCAGCTCTCTTGTTGCTTATATTTGGAGCGAT
ATTTTCAGAATTCAAGCAATTGAAAAAAAATGAAAAAATTATTCTTAAAA
AATGTGATAAAAGATATTCCAATGTTGATCGAAAATGTGATGTTGCATAT
GATGCAATTCGAAGAAATTGTTCCAATCTTCATCAGTCGTTGTCGAGTGC
TGTTAACAAAGCAAAGGAAAGAATAAACATACGATGCCAAATACCAATGA
CAGAAATTTGTTTAGCTTTAAGGAAAAAGTTCATTGAACAGCAATACCAA
GATTTTCTCAAATTAGAAAATCAATGTCAAAAAGCTTTGTTGCAAGTTGA
TAAATCATGTATTACCGCCCTTGATAGGGTTGACAGGTTATGCTCATCTG
TTTATAATAATATTGGTTGTTCGCTTTTCAGCTAAATTTTTCGTAATCTA
TGATTTTATAAAGATTTTTCAAAATGCTTGTAGTTTTAATTTATCAATTT
G
back to top

protein sequence of SMED30026803-orf-1

>SMED30026803-orf-1 ID=SMED30026803-orf-1|Name=SMED30026803-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
MKIFSALLLLIFGAIFSEFKQLKKNEKIILKKCDKRYSNVDRKCDVAYDA
IRRNCSNLHQSLSSAVNKAKERINIRCQIPMTEICLALRKKFIEQQYQDF
LKLENQCQKALLQVDKSCITALDRVDRLCSSVYNNIGCSLFS*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000035Category 3 cell
PLANA:0000099neuron
PLANA:0002032epidermal cell
PLANA:0002056medial muscle cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..17
score: 0.714