SMED30031521

Overview
NameSMED30031521
Smed IDSMED30031521
Length (bp)473
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 SMED30031521 (SMED30031521) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031521 (SMED30031521) 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 SMED30031521 (SMED30031521) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031521 (SMED30031521) 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



SMED30031521

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30031521h1SMcG0001803 SmedASXL_012958SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30031521h1SMcG0001803 Contig43533uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031521h1SMcG0001803 Contig43533newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30031521h1SMcG0001803 dd_Smed_v4_7792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30031521h1SMcG0001803 dd_Smed_v4_7792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30031521h1SMcG0001803 dd_Smed_v4_7792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30031521h1SMcG0001803 dd_Smed_v4_7792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30031521h1SMcG0001803 dd_Smed_v4_7792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30031521h1SMcG0001803 dd_Smed_v4_7792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30031521h1SMcG0001803 dd_Smed_v4_7792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30031521h1SMcG0001803 dd_Smed_v6_7792_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031521 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002177:15577..16049 -2320
Homology
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BLAST of SMED30031521 vs. TrEMBL
Match: A0A3S1AH33 (Integrase catalytic domain-containing protein OS=Elysia chlorotica OX=188477 GN=EGW08_000310 PE=4 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 1.047e-6
Identity = 39/137 (28.47%), Postives = 61/137 (44.53%), Query Frame = -2 
Query:   56 RPSGNGIIERNH*IIKFHAAKCHSHAQYIVFWRNVTLKDGKNQRTVSSDGLVNYHWR----------------FQSDIKVFVKLVTTKWTVRWPCGIVTGINSSTNIASHCENTFING*SSKISDVELNFEDDQIDD 418
            R SGNGI+ERNH  IK  + +        VFW N++ + G+ + T+    + +Y WR                F    +V+VK    K T +W  G V+ INS  N+        +NG   ++ D+     + + DD
Sbjct:  107 RASGNGIVERNHRTIKAISERGRVSPMKAVFWYNMSPRSGQKEATIPQRSVHSYSWRHPDVEPHIEPQESRSSFSIGDEVWVKPAAVKCTTQWEKGNVSKINSKNNVE-------VNGVPRRVLDLRQVVVNPEADD 236
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BLAST of SMED30031521 vs. Planmine SMEST
Match: SMESG000020506.1 (SMESG000020506.1)

HSP 1 Score: 70.4774 bits (171), Expect = 4.796e-15
Identity = 42/107 (39.25%), Postives = 54/107 (50.47%), Query Frame = -2 
Query:  146 A*RPSGNGIIERNH*IIKFHAAKCHSHAQYIVFWRNVTLKDGKNQRTVSSDGLVNYHWR--------------FQSDIKVFVKLVTTKWTVRWPCGIVTGINSSTNI 424
            A RPSGNGI+ERNH   K  A++  S  +  +FW NV LK   ++ +  ++ L NY WR              F+     FVK    K T  WP G +T INS TNI
Sbjct:   90 AYRPSGNGIVERNHRTTKCSASRSRSDPRDDIFWYNVALKLKGDKSSAPANRLFNYGWRFNIGNFLNVPHNSGFEECQSGFVKPYPFKCTTVWPMGTITAINSLTNI 196
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BLAST of SMED30031521 vs. Planmine SMEST
Match: SMESG000069076.1 (SMESG000069076.1)

HSP 1 Score: 48.521 bits (114), Expect = 4.645e-7
Identity = 30/95 (31.58%), Postives = 46/95 (48.42%), Query Frame = -2 
Query:   41 VSSDGLVNYHWRF--------------QSDIKVFVKLVTTKWTVRWPCGIVTGINSSTNIASHCENTFING*SSKISDVELNFEDDQIDDGNPRR 283
            + ++GL  YHW F              ++   V VK    K T +WP GIVTGINS+T+I        ++G S  +S++    ++D  DD +  R
Sbjct:  261 IRTEGLFKYHWIFYRGYEVENSVTCDYETGQMVVVKPAPAKCTTQWPIGIVTGINSATDIE-------VDGTSRHVSNIRPVVKEDMADDRSENR 348
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BLAST of SMED30031521 vs. Planmine SMEST
Match: SMESG000007937.1 (SMESG000007937.1)

HSP 1 Score: 45.4394 bits (106), Expect = 2.962e-6
Identity = 40/113 (35.40%), Postives = 45/113 (39.82%), Query Frame = -2 
Query:  149 A*RPSGNGIIERNH*IIKFHAAKCHSHAQYIVFWRNVTLKDGKNQRTVSSDGLVNYHWR----FQSDIK-----------------VFVKLVTTKWTVRWPCGIVTGINSSTN 424
            A RP  NGI ERNH  IK   A+         F  N+T   G +  TV S       WR    F +D                   VFVK    K   +W   IVTGINSSTN
Sbjct:   80 AYRPERNGITERNHSTIKRIVARSGCDPFKAGFIYNITPHSGLDSNTVPSMLHFGTEWRSPKLFLADTASESCDDYVHSHYTVGSHVFVKPPNAKCNTQWTVSIVTGINSSTN 192
[Close]
BLAST of SMED30031521 vs. Planmine SMEST
Match: SMESG000034856.1 (SMESG000034856.1)

HSP 1 Score: 45.0542 bits (105), Expect = 8.882e-6
Identity = 25/64 (39.06%), Postives = 34/64 (53.12%), Query Frame = -2 
Query:   41 KVFVKLVTTKWTVRWPCGIVTGINSSTNIASHCENTFING*SSKISDVELNFEDDQIDDGNPRR 232
            +V  KL   K T RWP   VTGINS+TNI        ++G S  +SD+    ++D  DD +  R
Sbjct:   58 RVVAKLALAKCTTRWPIRFVTGINSATNIE-------VDGTSKHVSDIRPVMDEDIADDNSKYR 114
The following BLAST results are available for this feature:
BLAST of SMED30031521 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 SMED30031521 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 SMED30031521 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 SMED30031521 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 SMED30031521 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 SMED30031521 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 SMED30031521 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 SMED30031521 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A3S1AH331.047e-628.47Integrase catalytic domain-containing protein OS=E... [more]
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BLAST of SMED30031521 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 SMED30031521 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 SMED30031521 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 SMED30031521 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 SMED30031521 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 SMED30031521 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000020506.14.796e-1539.25SMESG000020506.1[more]
SMESG000069076.14.645e-731.58SMESG000069076.1[more]
SMESG000007937.12.962e-635.40SMESG000007937.1[more]
SMESG000034856.18.882e-639.06SMESG000034856.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031521 ID=SMED30031521|Name=SMED30031521|organism=Schmidtea mediterranea sexual|type=transcript|length=473bp
AAGATAAGAGAGCTTCATTTGGTTACACACCGGATGTTTATCTTCTTGGA
TTTCCGTCATCAATCTGATCATCTTCAAAATTCAGTTCAACGTCGCTGAT
TTTACTGGATTATCCATTAATAAATGTATTTTCGCAATGTGACGCAATGT
TGGTGGACGAATTTATGCCAGTAACTATTCCACAAGGCCATCGAACAGTC
CATTTTGTAGTAACAAGCTTTACAAACACCTTGATGTCGCTCTGAAATCT
CCAATGGTAGTTAACCAATCCATCTGAAGAAACTGTTCTCTGATTTTTGC
CGTCTTTGAGTGTGACATTACGCCAAAAAACTATATACTGTGCGTGTGAA
TGACACTTGGCGGCATGGAATTTTATTATCTAGTGATTTCTCTCTATGAT
CCCGTTACCAGATGGCCGTTAAGCTAAAATTGCCGTTAAATTAAAATTGT
TAAAAAATAAATTAGTTTTGTTA
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