SMED30022870

Overview
NameSMED30022870
Smed IDSMED30022870
Length (bp)1570
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 SMED30022870 (SMED30022870) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022870 (SMED30022870) 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 SMED30022870 (SMED30022870) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022870 (SMED30022870) 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




SMED30022870

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30022870SMESG000079579.1 SmedASXL_076187SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
neuronSMED30022870SMESG000079579.1 dd_Smed_v4_16102_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30022870SMESG000079579.1 dd_Smed_v4_16102_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
headSMED30022870SMESG000079579.1 dd_Smed_v6_16102_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
neuronSMED30022870SMESG000079579.1 dd_Smed_v6_16102_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
GABAergic neuronSMED30022870SMESG000079579.1 dd_Smed_v6_16102_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
BLAST of SMED30022870 vs. Planmine SMEST
Match: SMESG000015664.1 (SMESG000015664.1)

HSP 1 Score: 103.99 bits (258), Expect = 8.236e-24
Identity = 68/167 (40.72%), Postives = 90/167 (53.89%), Query Frame = 1
Query:  643 QIQKLTTTCAIHFSVILLKDLIVKRLKVEPAD-----LMEIIKTIVYSIGYIPFYKETTALIEGSKISLLMIFTANRFY*ENSTHMKLRKCM*LSDRPKYLLPVVNANVTLIQNLSDFSMQPPLAEQKLNVLKPKTMISTV*AEPSVLAGHQTDFNSKNSLYPINSK 1128
            QIQKLT  C+IHFS +++  L  +++KV         L++   T +  +G+IP  K  T LI  SKI  L       F                 D+PKYLLP VN N+TL +N SD+S Q    E K+ +L+ K MI  V  EPSVLA HQ   NS+N++YPI SK
Sbjct:  242 QIQKLTIICSIHFSDVVV-GLNCQKIKVGNGRYTQKALIDCKNTCLAPMGFIPNDKVRTVLIAESKIVSLCSLLQIDFM----------------DQPKYLLPAVNVNITLKRNSSDYSTQSLTEEPKVKILEAKLMIRRVRVEPSVLAAHQIGLNSRNAIYPIRSK 391          
BLAST of SMED30022870 vs. Planmine SMEST
Match: SMESG000019398.1 (SMESG000019398.1)

HSP 1 Score: 85.5001 bits (210), Expect = 4.153e-22
Identity = 45/63 (71.43%), Postives = 49/63 (77.78%), Query Frame = 3
Query:  534 EFKITGSPTLYLNLNDTLWYIKSKVTNRNGKELPVISNTKANNYLCHTFFSDIVEGLNSQKIE 722
            EFKITGS T Y++LNDTL YIK KVTN NGKEL   S+ KANNYL HT FSD+V  LNSQ IE
Sbjct:  264 EFKITGSHTEYIDLNDTLLYIKLKVTNNNGKELLTSSDAKANNYLFHTLFSDVVVRLNSQMIE 326          

HSP 2 Score: 38.5058 bits (88), Expect = 4.153e-22
Identity = 22/42 (52.38%), Postives = 27/42 (64.29%), Query Frame = 2
Query:  374 KILKQRXXXXXXYIRIRVYGKTDLRNFHRQTLQMVMEYGTFE 499
            K+ KQ+N+   NYIRI + GKT+L  F R   Q V EY TFE
Sbjct:  207 KVYKQKNDRVWNYIRIMICGKTELCIFDRPASQAVREYATFE 248          

HSP 3 Score: 85.5001 bits (210), Expect = 7.450e-19
Identity = 45/63 (71.43%), Postives = 49/63 (77.78%), Query Frame = 3
Query:  534 EFKITGSPTLYLNLNDTLWYIKSKVTNRNGKELPVISNTKANNYLCHTFFSDIVEGLNSQKIE 722
            EFKITGS T Y++LNDTL YIK KVTN NGKEL   S+ KANNYL HT FSD+V  LNSQ IE
Sbjct:  714 EFKITGSHTEYIDLNDTLLYIKLKVTNNNGKELLTSSDAKANNYLFHTLFSDVVVRLNSQMIE 776          

HSP 4 Score: 27.7202 bits (60), Expect = 7.450e-19
Identity = 14/27 (51.85%), Postives = 16/27 (59.26%), Query Frame = 2
Query:  419 IRVYGKTDLRNFHRQTLQMVMEYGTFE 499
            I + GKT+L  F R   Q V EY TFE
Sbjct:  672 IMICGKTELCIFDRPASQAVREYATFE 698          

HSP 5 Score: 64.3142 bits (155), Expect = 1.539e-10
Identity = 56/147 (38.10%), Postives = 77/147 (52.38%), Query Frame = 1
Query:  691 LLKDLIVKRLKVEPADLMEIIK-TIVYSIGYIPFYKETTALIEGSKISLLMIFTANRFY*ENSTHMKLRKCM*LSDRPKYLLPVVNANVTLIQNLSDFSMQPPLAEQKLNVLKPKTMISTV*AEPSVLAGHQTDFNSKNSLYPINSK 1128
            L  D++V RL    + ++E  K T + S+GYI   K  TALI  SKI  L             + +++       D  KYL P V  N+TL +N SD+S+Q    + K+ +L+ K MI  V  EP VLA HQ    SKN++YPI SK
Sbjct:  762 LFSDVVV-RLN---SQMIEDCKNTCLTSMGYILNDKARTALIAESKIVSL------------CSSLQID----FMDHQKYLHPGVILNITLKRNSSDYSIQSLTEDPKVKILEAKLMIRRVRVEPYVLARHQIGLISKNAIYPIISK 888          

HSP 6 Score: 62.7734 bits (151), Expect = 4.520e-10
Identity = 54/144 (37.50%), Postives = 75/144 (52.08%), Query Frame = 1
Query:  691 LLKDLIVKRLKVEPADLMEIIK-TIVYSIGYIPFYKETTALIEGSKISLLMIFTANRFY*ENSTHMKLRKCM*LSDRPKYLLPVVNANVTLIQNLSDFSMQPPLAEQKLNVLKPKTMISTV*AEPSVLAGHQTDFNSKNSLYPI 1119
            L  D++V RL    + ++E  K T + S+GYI   K  TALI  SKI  L             + +++       D  KYL P V  N+TL +N SD+S+Q    + K+ +L+ K MI  V  EP VLA HQ    SKN++YPI
Sbjct:  312 LFSDVVV-RLN---SQMIEDCKNTCLTSMGYILNDKARTALIAESKIVSL------------CSSLQID----FMDHQKYLHPGVILNITLKRNSSDYSIQSLTEDPKVKILEAKLMIRRVRVEPYVLARHQIGLISKNAIYPI 435          
BLAST of SMED30022870 vs. Planmine SMEST
Match: SMESG000060157.1 (SMESG000060157.1)

HSP 1 Score: 65.0846 bits (157), Expect = 4.852e-13
Identity = 34/65 (52.31%), Postives = 42/65 (64.62%), Query Frame = 3
Query:  534 EFKITGSPTLYLNLNDTLWYIKSKVTNRNGKELPVISNTKANNYLCHTFFSDIVEGLNSQKIEGG 728
            EF I GS T YL+LNDTL  ++ KV N + K+L   S+ K NNY+ HT F D + G N  KIEGG
Sbjct:   42 EFYINGSQTEYLDLNDTLLTVQIKVVNIDTKKLVDTSDVKPNNYMFHTLFKDAIFGFNHIKIEGG 106          

HSP 2 Score: 28.1054 bits (61), Expect = 4.852e-13
Identity = 12/25 (48.00%), Postives = 17/25 (68.00%), Query Frame = 2
Query:  425 VYGKTDLRNFHRQTLQMVMEYGTFE 499
            + GK++L  F R + Q V+EYG FE
Sbjct:    2 ICGKSELCIFDRSSPQAVIEYGVFE 26          
BLAST of SMED30022870 vs. Planmine SMEST
Match: SMESG000076652.1 (SMESG000076652.1)

HSP 1 Score: 60.8474 bits (146), Expect = 6.899e-13
Identity = 33/65 (50.77%), Postives = 42/65 (64.62%), Query Frame = 3
Query:  534 EFKITGSPTLYLNLNDTLWYIKSKVTNRNGKELPVISNTKANNYLCHTFFSDIVEGLNSQKIEGG 728
            EF I GS T YL+LNDTL  ++ KV +++ K L   S+   NN+L HT F D V G N+ KIEGG
Sbjct:  467 EFYINGSQTEYLDLNDTLLTVQIKVVDKDRKLLGEPSDVIPNNFLFHTLFKDAVLGFNNIKIEGG 531          

HSP 2 Score: 31.9574 bits (71), Expect = 6.899e-13
Identity = 42/141 (29.79%), Postives = 55/141 (39.01%), Query Frame = 2
Query:  110 RRQTTIFGRKQYGS*WLKTIGQLLEICL*K--------PLKIIMNNVKILASLKSNALI*IHRCYIRCNLFVTKCNGIK*FI*I*I*KA*TPT*TRKILK---QRXXXXXXYIRIRVYGKTDLRNFHRQTLQMVMEYGTFE 499
            +   T+  RK  G  WL+TIG+     L +           +IMN  KIL SLKSNAL  + +          K                 P   RK      Q      NYI   + GK++L  F R + Q V+E G FE
Sbjct:  327 KTHLTLHFRKLDG--WLRTIGRFALPILKRIGSFGMKTAKDVIMNEQKILPSLKSNALSELGKVLPSVAGMFQKPEA--------------PAQKRKRHHEHLQTKERAWNYISKMICGKSELCLFDRPSPQAVIEMGAFE 451          

HSP 3 Score: 56.9954 bits (136), Expect = 3.541e-8
Identity = 29/72 (40.28%), Postives = 44/72 (61.11%), Query Frame = 1
Query:  913 DRPKYLLPVVNANVTLIQNLSDFSMQPPLAEQKLNVLKPKTMISTV*AEPSVLAGHQTDFNSKNSLYPINSK 1128
            D+PKYLL  VN ++ L ++ S  S+        L ++  K ++  V  EPSVLAGHQ   NSK+++YP+ +K
Sbjct:  589 DQPKYLLLCVNVHIRLKRSDSALSLTSATTAPILQLVDAKLLVRRVRVEPSVLAGHQLGLNSKHAIYPLKTK 660          
BLAST of SMED30022870 vs. Planmine SMEST
Match: SMESG000048922.1 (SMESG000048922.1)

HSP 1 Score: 61.6178 bits (148), Expect = 7.925e-12
Identity = 33/65 (50.77%), Postives = 42/65 (64.62%), Query Frame = 3
Query:  534 EFKITGSPTLYLNLNDTLWYIKSKVTNRNGKELPVISNTKANNYLCHTFFSDIVEGLNSQKIEGG 728
            EF I GS T YL+LNDTL  ++ KV +++ K L   S+   NN+L HT F D V G N+ KIEGG
Sbjct:  458 EFYINGSQTEYLDLNDTLLTVQIKVVDKDRKPLGEPSDVIPNNFLFHTLFKDAVLGFNNIKIEGG 522          

HSP 2 Score: 27.7202 bits (60), Expect = 7.925e-12
Identity = 36/124 (29.03%), Postives = 51/124 (41.13%), Query Frame = 2
Query:  155 WLKTIGQ--------LLEICL*KPLKIIMNNVKILASLKSNALI*IHRCYIR-CNLFVTKCNGIK*FI*I*I*KA*TPT*TRKILKQRXXXXXXYIRIRVYGKTDLRNFHRQTLQMVMEYGTFE 499
            WL+TIG+        L    +     +IMN  KIL SLKSNAL  + +       +F  + +G                 T       +    NYI   + GK++L  F R + Q V+E G FE
Sbjct:  334 WLRTIGRFALPILKRLGSFGMKTSKDVIMNEQKILPSLKSNALSELGKVLPSVAGMFQKQVSGTS---------------TGTSTGTNSKTTWNYISKMICGKSELCLFDRPSPQAVIEMGVFE 442          
The following BLAST results are available for this feature:
BLAST of SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 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 SMED30022870 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000015664.18.236e-2440.72SMESG000015664.1[more]
SMESG000019398.14.153e-2271.43SMESG000019398.1[more]
SMESG000060157.14.852e-1352.31SMESG000060157.1[more]
SMESG000076652.16.899e-1350.77SMESG000076652.1[more]
SMESG000048922.17.925e-1250.77SMESG000048922.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022870 ID=SMED30022870|Name=SMED30022870|organism=Schmidtea mediterranea sexual|type=transcript|length=1570bp
CGGAAATGGAATTCGATTTGCAAACGATTCAAAAACACTTATAACTTTTC
GTTCTCGAAATTAAGATGTCTAATCCTTAAATAATTTCTCTCTATATCAA
TAGTCCAACCGGCGTCAAACTACAATATTTGGACGGAAACAATATGGTTC
TTGATGGTTAAAAACTATTGGTCAACTCTTGGAAATTTGTTTATGAAAAC
CGCTAAAGATAATAATGAACAATGTCAAAATATTAGCATCCTTAAAATCT
AATGCTTTAATCTGAATTCATAGATGCTATATCAGATGTAATTTATTCGT
TACCAAATGTAATGGAATCAAATGATTCATCTGAATCTGAATCTGAAAAG
CCTGAACCCCAACCTAGACGAGGAAAATATTGAAACAAAGAAATAACGGG
AATTAGAACTATATACGAATAAGGGTTTACGGAAAAACTGATTTACGTAA
TTTTCATAGACAGACGCTTCAAATGGTAATGGAATACGGGACATTTGAAT
ATGTATTTCTATTTATTTTAATTGTTGACATTTGAATTTAAGATTACTGG
TTCTCCTACTCTATACCTTAATTTGAATGATACATTATGGTACATTAAAT
CGAAGGTTACAAATAGAAATGGAAAAGAATTACCAGTTATTTCAAATACA
AAAGCTAACAACTACTTGTGCCATACATTTTTCAGTGATATTGTTGAAGG
ACTTAATAGTCAAAAGATTGAAGGTGGAACCGGCAGATCTAATGGAAATA
ATCAAAACAATTGTTTACTCTATAGGTTATATTCCATTTTATAAAGAAAC
AACAGCTTTAATTGAGGGTTCAAAAATAAGTTTACTAATGATATTTACTG
CAAATCGATTTTATTAAGAAAACAGTACTCATATGAAATTAAGAAAATGC
ATGTGATTGTCAGATCGACCAAAATACTTACTTCCAGTAGTTAATGCTAA
TGTAACATTAATACAAAATTTATCAGATTTTAGTATGCAACCTCCATTAG
CCGAACAAAAGTTAAATGTATTGAAACCAAAAACGATGATTAGCACAGTT
TGAGCAGAACCCTCTGTTTTAGCCGGACATCAAACTGATTTTAATTCAAA
AAATTCTTTATATCCAATTAACAGTAAATATTGAAAAAATTGGTTCTAGG
TGTAAATTCAACAATTTGAAATCAAGATAATGAGGATGAGACTGTTCAAA
GTAAGAGGATCTAGTCGGTTGAATAACGTTATTTAAAGGGTAAATATTAT
CTAAATGGGGAATATAGAGTATTTTATTGAATCAAAAAATATTGAATAAG
GAGTGGAGAATAAATAGGCTAGAAATATTGTTATTAAACAAAGGAATTTA
AAATTTTTTAAAGAGGTCTTGAAAGTTGAATATTTAATTTTATTCAAGAG
GATACTTTAAGAAAATAGGTATATAGTCAATCATTCGAGGGTGAATCATA
ATATATCTGTTGAGTTAATATTTTATTTAGTTCGGTAGGAACTGTTTGCT
TTGACTCCACCTGTTCTTTATATCAGTGCTTCCCAACGTTTTTCAGTCTA
CGGCACTGTAACTATTTTGT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000464GABAergic neuron