SMED30020939

Overview
NameSMED30020939
Smed IDSMED30020939
Length (bp)630
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30020939 (SMED30020939) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020939 (SMED30020939) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30020939

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30020939 SmedASXL_061098SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30020939 SmedASXL_061098SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020939 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005420:15194..15823 -3060
v31.020937:10419..11048 +2976
v31.014959:4823..5455 -2349
Homology
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BLAST of SMED30020939 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 239.58 bits (610), Expect = 1.964e-79
Identity = 140/189 (74.07%), Postives = 155/189 (82.01%), Query Frame = -1 
Query:    1 MNLPRIPKISPTPSAVAAAQYLEKLERENFAIREKYNKLKGTWCSPEATRELYKKITWLSRSRDDLITENRSQRITISNKSAALRQIFTEKELQVRLPSRNMAQRLDIIQAHHL*TNPKDQRDNNNPDVLTELSTPSTVXXXXXXXXXXXXRQV*SRK--CTPTSKSV*ENASLESITELFGPKPIALN 561
            MNLPRIPKISP PSAVA AQYLEKLERENF +REKYN+LK TWCSPE TRE YKKI  LSR+RDDLI ENRSQRI IS + AA RQIFTEKE Q RLPSRNM QRLDII  HHL TNPK+QRDNNN +V T+L+TPSTVN+RH+PN+NRRRRQ    +     ++  V ENASLESITELF P+PIALN
Sbjct:    1 MNLPRIPKISPAPSAVAEAQYLEKLERENFTLREKYNRLKVTWCSPEITRERYKKINRLSRARDDLIIENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITELFWPQPIALN 189
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BLAST of SMED30020939 vs. Planmine SMEST
Match: SMESG000004294.1 (SMESG000004294.1)

HSP 1 Score: 221.861 bits (564), Expect = 4.709e-74
Identity = 123/199 (61.81%), Postives = 135/199 (67.84%), Query Frame = -1 
Query:    1 MNLPRIPKISPTPSAVAAAQYLEKLERENFAIREKYNKLKGTWCSPEATRELYKKITWLSRSRDDLITENRSQRITISNKSAALRQIFTEKELQVRLPSRNMAQRLDIIQAHHL*TNPKDQRDNNNPDVLTELSTPSTVXXXXXXXXXXXXRQV*SRKCTP------------TSKSV*ENASLESITELFGPKPIALN 561
            MNLPRIPKISP PSAVAAAQYLEKLERENFA+REKYNKLK TWCS EATRELYK IT LSR+RDDLI ENRSQRITIS+++A LRQIFTEKELQ RLPSRNM QRLDII AHHL  NP++QRD   P+                            R+C P             +  V ENASL S+TELFG +P  LN
Sbjct:    1 MNLPRIPKISPPPSAVAAAQYLEKLERENFALREKYNKLKFTWCSTEATRELYKMITRLSRARDDLIIENRSQRITISDQNATLRQIFTEKELQARLPSRNMVQRLDIILAHHLSKNPENQRDYWPPNC---------------------------RRCQPEIGVRAENTLIQANLGVRENASLGSVTELFGLEPTVLN 172
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BLAST of SMED30020939 vs. Planmine SMEST
Match: SMESG000062943.1 (SMESG000062943.1)

HSP 1 Score: 199.134 bits (505), Expect = 1.449e-65
Identity = 96/125 (76.80%), Postives = 108/125 (86.40%), Query Frame = -1 
Query:  187 MNLPRIPKISPTPSAVAAAQYLEKLERENFAIREKYNKLKGTWCSPEATRELYKKITWLSRSRDDLITENRSQRITISNKSAALRQIFTEKELQVRLPSRNMAQRLDIIQAHHL*TNPKDQRDNN 561
            MNL RIP+I+P PS VAAAQY EKL+RENF +REKYNKLK TWCSPEAT+EL KKITWLSR+RDDLI +NR QRITIS++SAALRQIFTEKELQ RLPSRNM QRLDII AHHL  N +  ++NN
Sbjct:    1 MNLRRIPRIAPAPSTVAAAQYAEKLKRENFTLREKYNKLKCTWCSPEATKELIKKITWLSRARDDLIIKNRGQRITISDQSAALRQIFTEKELQARLPSRNMTQRLDIIPAHHLPANSEGSKENN 125
[Close]
BLAST of SMED30020939 vs. Planmine SMEST
Match: SMESG000038817.1 (SMESG000038817.1)

HSP 1 Score: 191.045 bits (484), Expect = 1.070e-61
Identity = 96/135 (71.11%), Postives = 113/135 (83.70%), Query Frame = -1 
Query:  157 MNLPRIPKISPTPSAVAAAQYLEKLERENFAIREKYNKLKGTWCSPEATRELYKKITWLSRSRDDLITENRSQRITISNKSAALRQIFTEKELQVRLPSRNMAQRLDIIQAHHL*TNPKDQRDNNNPDVLTELST 561
            MNLPRIPKISP  SAVAA Q +EK +RENF + EKYNKLKGTW SPEAT+ELYKKI  LS++ DDL+ EN+SQ IT++++SAALR+IFTEK+LQ RLPSRNMAQRLDII  HHL TNP+D R N N +VL EL+T
Sbjct:    1 MNLPRIPKISPALSAVAATQCVEKPKRENFTLPEKYNKLKGTWWSPEATKELYKKIMRLSQALDDLMIENQSQWITVADQSAALREIFTEKKLQARLPSRNMAQRLDIIPTHHLPTNPEDSRTNYNANVLVELAT 135
[Close]
BLAST of SMED30020939 vs. Planmine SMEST
Match: SMESG000021151.1 (SMESG000021151.1)

HSP 1 Score: 175.637 bits (444), Expect = 1.421e-54
Identity = 88/131 (67.18%), Postives = 106/131 (80.92%), Query Frame = -1 
Query:  178 MNLPRIPKISPTPSAVAAAQYLEKLERENFAIREKYNKLKGTWCSPEATRELYKKITWLSRSRDDLITENRSQRITISNKSAALRQIFTEKELQVRLPSRNMAQRLDIIQAHHL*TNPKDQ---RDNNNPD 561
            MNLP I +I   P AVA  Q LE LERENF IREKY K+KGTWCSP+AT+EL+KKIT LSR RDDL+ E RSQ++TIS +SAALRQIFTEKELQ RLPSRN+AQ+++II AHHL TN ++Q   +DN+ P+
Sbjct:    1 MNLPSIIRIVRAPYAVAMNQRLESLERENFIIREKYEKIKGTWCSPDATKELHKKITSLSRDRDDLVIETRSQQVTISEQSAALRQIFTEKELQARLPSRNLAQQINIIPAHHLPTNAENQAINQDNSTPE 131
The following BLAST results are available for this feature:
BLAST of SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 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 SMED30020939 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046646.11.964e-7974.07SMESG000046646.1[more]
SMESG000004294.14.709e-7461.81SMESG000004294.1[more]
SMESG000062943.11.449e-6576.80SMESG000062943.1[more]
SMESG000038817.11.070e-6171.11SMESG000038817.1[more]
SMESG000021151.11.421e-5467.18SMESG000021151.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020939 ID=SMED30020939|Name=SMED30020939|organism=Schmidtea mediterranea sexual|type=transcript|length=630bp
ATTCAAGGCTATTGGTTTCGGCCCAAATAGTTCCGTGATACTCTCTAGAC
TGGCATTTTCTCAAACAGATTTGCTTGTAGGAGTGCATTTTCGGCTCTAC
ACTTGTCGTCTTCGTCGGTTCTTATTGGGCTTGTGACGCCGATTTACGGT
TGATGGGGTTGACAGTTCGGTGAGCACATCCGGGTTGTTATTATCTCTTT
GATCTTTGGGATTTGTCTACAGGTGATGTGCCTGGATGATGTCCAGGCGT
TGAGCCATATTACGACTCGGCAGTCGCACTTGCAATTCCTTTTCAGTGAA
TATCTGCCGGAGCGCGGCGCTCTTGTTAGATATCGTAATACGCTGACTCC
GGTTTTCTGTTATAAGATCATCGCGGGACCGAGAAAGCCACGTGATCTTC
TTATACAGCTCCCTCGTAGCTTCTGGGGAGCACCAGGTGCCTTTTAGTTT
ATTGTATTTTTCTCGGATTGCAAAATTTTCTCGCTCCAGTTTTTCTAGAT
ACTGGGCAGCAGCAACGGCTGATGGAGTTGGGGAGATTTTCGGTATTCTG
GGTAGATTCATCTTGATTAATCGATTGGGTTTCTATAGGCAGGAGATTTG
ATGGGGTTTGAGAATGCTATGATAGTACAA
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protein sequence of SMED30020939-orf-1

>SMED30020939-orf-1 ID=SMED30020939-orf-1|Name=SMED30020939-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
MNLPRIPKISPTPSAVAAAQYLEKLERENFAIREKYNKLKGTWCSPEATR
ELYKKITWLSRSRDDLITENRSQRITISNKSAALRQIFTEKELQVRLPSR
NMAQRLDIIQAHHL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell