SMED30020396

Overview
NameSMED30020396
Smed IDSMED30020396
Length (bp)571
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 SMED30020396 (SMED30020396) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020396 (SMED30020396) 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 SMED30020396 (SMED30020396) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020396 (SMED30020396) 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



SMED30020396

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



PAGE Curations: 20

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30020396SMESG000046779.1 SMESG000024881.1 SmedASXL_013664SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
Category 2 cellSMED30020396SMESG000046779.1 SMESG000024881.1 SmedASXL_013664SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		whole organism asexual adult fluorescence in situ hybridization evidence
X1 cellSMED30020396SMESG000046779.1 SMESG000024881.1 SmedASXL_013664SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30020396SMESG000046779.1 SMESG000024881.1 SmedASXL_013664SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
parenchymaSMED30020396SMESG000046779.1 SMESG000024881.1 SmedASXL_013664SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30020396SMESG000046779.1 SMESG000024881.1 dd_Smed_v4_478_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020396SMESG000046779.1 SMESG000024881.1 dd_Smed_v4_478_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020396SMESG000046779.1 SMESG000024881.1 dd_Smed_v4_478_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020396SMESG000046779.1 SMESG000024881.1 dd_Smed_v4_478_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020396SMESG000024881.1 Contig52165newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020396SMESG000024881.1 Contig52165uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020396SMESG000024881.1 Contig52496newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020396SMESG000024881.1 Contig52496uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30020396SMESG000046779.1 SMESG000024881.1 dd_Smed_v6_478_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Category 2 cellSMED30020396SMESG000046779.1 SMESG000024881.1 dd_Smed_v6_478_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30020396SMESG000046779.1 SMESG000024881.1 dd_Smed_v4_478_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020396SMESG000046779.1 SMESG000024881.1 SMED_01113_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020396SMESG000046779.1 SMESG000024881.1 SMED_01113_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020396SMESG000024881.1 SMED_01113_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020396SMESG000024881.1 SMED_01113_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020396 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005203:11468..12085 -2733
v31.007338:23205..23820 +2690
v31.003620:2728..3343 +2681
v31.002227:66585..67202 -2193
v31.013613:14934..15449 +1348
v31.013603:2810..3325 -1330
v31.008660:29039..29620 +1313
v31.021348:9778..10360 -1294
Homology
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BLAST of SMED30020396 vs. TrEMBL
Match: J7GX15 (PROG-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 65.855 bits (159), Expect = 1.092e-9
Identity = 39/96 (40.62%), Postives = 52/96 (54.17%), Query Frame = 2 
Query:  179 TECEDEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKCQETPTKAGRKVVRDLEKQIFGDYDKLDKTCDPQYAALDKECLEQYQQLD 466
             +C   YEE DK CDP Y  LDK C  +YV+   D+ K+  + + KC     K  R  +R LE    G YD +D  CD +Y ALDK C  +Y ++D
Sbjct:  115 ADCMKLYEETDKYCDPLYLKLDKDCDCRYVKALNDYTKRWDSYHSKCGSKYDKKCRTELRALENWFNGLYDSIDGHCDAEYDALDKYCDVEYNKVD 210
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BLAST of SMED30020396 vs. Planmine SMEST
Match: SMESG000024881.1 (SMESG000024881.1)

HSP 1 Score: 295.434 bits (755), Expect = 7.450e-104
Identity = 148/150 (98.67%), Postives = 149/150 (99.33%), Query Frame = 2 
Query:   62 MFALAIVNVQCRFRYRNIRDFAKKEDLDNKCKELNAKVDTECEDEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKCQETPTKAGRKVVRDLEKQIFGDYDKLDKTCDPQYAALDKECLEQYQQLDKHCLPLYAQQKKCER 511
            MFALAIVNVQCRFRYRNIRDFAKKEDLDNKCKELNAKVDTECEDEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKCQETPTKAGRKVVRDLEKQIFGDYDKLDKTCDPQYAALDKECLEQYQ+LDKHCLPLY QQKKCER
Sbjct:    1 MFALAIVNVQCRFRYRNIRDFAKKEDLDNKCKELNAKVDTECEDEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKCQETPTKAGRKVVRDLEKQIFGDYDKLDKTCDPQYAALDKECLEQYQKLDKHCLPLYEQQKKCER 150
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BLAST of SMED30020396 vs. Planmine SMEST
Match: SMESG000070435.1 (SMESG000070435.1)

HSP 1 Score: 99.7525 bits (247), Expect = 1.842e-27
Identity = 59/79 (74.68%), Postives = 65/79 (82.28%), Query Frame = 2 
Query:   83 NVQCRFRYRNIRDFAKKEDLDNKCKELNAKVDTECEDEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKC 319
            N   +    +I DF+KKEDLDN CK+ N+KVDTECEDE EEL KLCD KYEALDK+CLPKYVQIN DFAKQVVNANLKC
Sbjct:   19 NYPIKLHLISILDFSKKEDLDNNCKDFNSKVDTECEDECEELGKLCDTKYEALDKECLPKYVQINGDFAKQVVNANLKC 97
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BLAST of SMED30020396 vs. Planmine SMEST
Match: SMESG000046779.1 (SMESG000046779.1)

HSP 1 Score: 90.5077 bits (223), Expect = 4.743e-24
Identity = 43/48 (89.58%), Postives = 45/48 (93.75%), Query Frame = 1 
Query:    1 INITNILLNHYLQYEINYFDYVCSGHRECPMQIPIPKYPRFCQEGRPR 144
            INITNILLN  LQYEINYF+YVCSGHRECPMQIPIPKY RFCQ+GRPR
Sbjct:   34 INITNILLNRNLQYEINYFNYVCSGHRECPMQIPIPKYLRFCQKGRPR 81
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BLAST of SMED30020396 vs. Planmine SMEST
Match: SMESG000024707.1 (SMESG000024707.1)

HSP 1 Score: 66.2402 bits (160), Expect = 2.162e-13
Identity = 39/97 (40.21%), Postives = 53/97 (54.64%), Query Frame = 2 
Query:  179 TECEDEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKCQETPTKAGRKVVRDLEKQIFGDYDKLDKTCDPQYAALDKECLEQYQQLDK 469
             +C   YEE DK CDP Y  LDK C  +YV+   D+ K+  + + KC     K  R  +R LE    G YD +D  CD +Y ALDK C  +Y ++D+
Sbjct:  107 ADCMKLYEETDKYCDPLYLKLDKDCDCRYVKALNDYTKRWDSYHSKCGSKYDKKCRTELRALENWFNGLYDSIDGHCDAEYDALDKYCDVEYNKVDQ 203
[Close]
BLAST of SMED30020396 vs. Planmine SMEST
Match: SMESG000024882.1 (SMESG000024882.1)

HSP 1 Score: 65.855 bits (159), Expect = 3.067e-13
Identity = 39/96 (40.62%), Postives = 52/96 (54.17%), Query Frame = 2 
Query:  179 TECEDEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKCQETPTKAGRKVVRDLEKQIFGDYDKLDKTCDPQYAALDKECLEQYQQLD 466
             +C   YEE DK CDP Y  LDK C  +YV+   D+ K+  + + KC     K  R  +R LE    G YD +D  CD +Y ALDK C  +Y ++D
Sbjct:  115 ADCMKLYEETDKYCDPLYLKLDKDCDCRYVKALNDYTKRWDSYHSKCGSKYDKKCRTELRALENWFNGLYDSIDGHCDAEYDALDKYCDVEYNKVD 210
The following BLAST results are available for this feature:
BLAST of SMED30020396 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 SMED30020396 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 SMED30020396 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 SMED30020396 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 SMED30020396 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 SMED30020396 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 SMED30020396 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 SMED30020396 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
J7GX151.092e-940.63PROG-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=... [more]
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BLAST of SMED30020396 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 SMED30020396 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 SMED30020396 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 SMED30020396 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 SMED30020396 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 SMED30020396 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000024881.17.450e-10498.67SMESG000024881.1[more]
SMESG000070435.11.842e-2774.68SMESG000070435.1[more]
SMESG000046779.14.743e-2489.58SMESG000046779.1[more]
SMESG000024707.12.162e-1340.21SMESG000024707.1[more]
SMESG000024882.13.067e-1340.63SMESG000024882.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020396 ID=SMED30020396|Name=SMED30020396|organism=Schmidtea mediterranea sexual|type=transcript|length=571bp
ATAAATATCACAAATATTTTGCTTAACCATTATTTGCAATATGAAATTAA
TTATTTTGATTATGTTTGCTCTGGCCATCGTGAATGTCCAATGCAGATTC
CGATACCGAAATATCCGAGATTTTGCCAAGAAGGAAGACCTCGATAATAA
ATGCAAAGAACTCAATGCAAAAGTCGACACGGAATGTGAGGATGAATATG
AAGAGCTGGACAAATTGTGCGATCCAAAATATGAAGCATTGGACAAACAA
TGTTTGCCGAAATATGTTCAAATCAATGCAGATTTTGCCAAGCAAGTTGT
AAATGCAAATTTGAAATGTCAAGAAACTCCGACGAAAGCTGGTCGAAAGG
TTGTAAGAGATTTGGAAAAGCAGATTTTCGGCGATTACGACAAACTGGAC
AAGACCTGTGACCCGCAATATGCAGCATTAGATAAGGAATGTTTGGAACA
ATACCAACAGCTGGATAAGCATTGCCTGCCATTGTATGCACAACAGAAGA
AATGTGAAAGGCGTTGAAATAATTGAAAATGTTGTGTAAAATATAAATAT
AAATTTCTGAATAAAAAAAAG
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protein sequence of SMED30020396-orf-1

>SMED30020396-orf-1 ID=SMED30020396-orf-1|Name=SMED30020396-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=159bp
MKLIILIMFALAIVNVQCRFRYRNIRDFAKKEDLDNKCKELNAKVDTECE
DEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKCQETPTKA
GRKVVRDLEKQIFGDYDKLDKTCDPQYAALDKECLEQYQQLDKHCLPLYA
QQKKCERR*
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Aliases
The feature 'SMED30020396' has the following synonyms
Synonym
prog1-1
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0000418head
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0002075pigment cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0002142parenchyma
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 31..51
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.775