SMED30028921

Overview
NameSMED30028921
Smed IDSMED30028921
Length (bp)496
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 SMED30028921 (SMED30028921) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028921 (SMED30028921) 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 SMED30028921 (SMED30028921) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028921 (SMED30028921) 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



SMED30028921

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30028921SMESG000024592.1 SMESG000013347.1 dd_Smed_v4_1308_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30028921SMESG000024592.1 SMESG000013347.1 dd_Smed_v4_1308_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30028921SMESG000024592.1 SMESG000013347.1 dd_Smed_v6_1308_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
intestinal phagocyteSMED30028921SMESG000024592.1 SMESG000013347.1 dd_Smed_v6_1308_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
Alignments
SMED30028921 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005341:1128..1617 -1649
v31.000276:146107..146557 -1350
v31.007552:3878..4374 +1328
v31.005719:22746..23220 -1320
v31.002109:2679..3097 -1320
v31.000118:185264..185715 -1314
v31.020379:2911..3361 +1311
v31.010362:10447..10905 +1302
v31.001695:53722..54190 +1302
v31.007413:16587..17028 -1297
v31.002909:39387..39825 +1297
v31.001317:38093..38547 -1297
v31.018962:8358..8823 -1296
v31.005631:20203..20637 +1295
v31.001667:103541..103985 -1290
v31.002294:33139..33604 +1277
v31.007324:19773..20200 -1274
v31.002636:2122..2524 -1270
v31.018521:12628..13169 +1268
v31.000798:85547..85992 -1268
v31.000058:234648..235103 +1266
v31.007487:20620..21051 -1261
v31.002139:3791..4262 -1256
v31.044558:673..1154 +1242
v31.022420:11630..12116 +1241
v31.025467:7801..8211 -1238
v31.022530:6961..7447 +1236
v31.019607:13917..14357 +1226
v31.017215:3618..4063 -1226
v31.003606:35390..35876 +1226
v31.030732:2248..2726 +1224
v31.011551:21843..22326 -1218
v31.000314:97277..97788 -1211
v31.014872:2258..2675 +1207
v31.024303:3130..3547 -1203
v31.012237:22134..22577 +1203
v31.003121:27798..28249 +1201
v31.005110:15293..15724 +1200
v31.002735:46608..47069 -1195
v31.008118:29711..30165 -1192
v31.029163:9297..9746 -1190
v31.006026:25955..26372 -1189
v31.003852:48114..48583 +1187
v31.002348:29185..29644 -1183
v31.011923:13487..13961 -1181
v31.000292:113787..114223 -1181
v31.001118:13278..13698 -1178
v31.000169:125967..126381 +1174
v31.015075:11882..12326 -1173
v31.000074:184968..185445 -1172
v31.012294:11709..12363 +1167
v31.026534:5541..5985 +1165
v31.000732:104992..105412 -1161
v31.002059:25853..26265 -1160
v31.000742:15369..15842 +1160
v31.000402:61563..62047 -1158
v31.002292:51391..51789 +1156
v31.000609:45848..46296 -1155
v31.001437:19331..19776 +1154
v31.018144:9080..9523 +1152
v31.001875:55399..55824 +1149
v31.020934:12560..12993 -1142
v31.033844:3538..3963 -1139
v31.012433:3959..4428 +1139
v31.003937:38020..40601 +1139
v31.010891:9045..9512 +1131
v31.002911:31198..31685 -1131
v31.003937:38005..38423 +1130
v31.002491:6265..6772 +1126
v31.000446:51722..52183 +1124
v31.002629:23732..24130 +1119
v31.000422:35697..36094 +1119
v31.001472:87553..88022 -1118
v31.007753:592..1033 -1112
v31.000624:171561..171996 -1102
v31.010080:6464..6901 +1093
v31.002886:27490..27953 +1091
v31.012140:20766..21203 +1089
v31.001126:61718..62192 +1089
v31.002979:46299..46752 -1084
v31.001597:41003..41422 -1072
v31.005092:8604..9029 +1070
v31.035265:1344..1766 -1064
v31.009527:19552..20007 -1060
v31.047828:311..696 -1055
v31.011723:5967..6352 -1055
v31.000057:150519..150935 +1043
v31.008429:3759..4208 +1022
v31.014872:12846..13271 -988
v31.000068:71663..72114 -923
v31.002737:14103..14558 +819
Homology
The following BLAST results are available for this feature:
BLAST of SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 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 SMED30028921 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028921 ID=SMED30028921|Name=SMED30028921|organism=Schmidtea mediterranea sexual|type=transcript|length=496bp
TTATATATCTCATATTCACACCGTCCACGACTACAAACAATATTTATCCA
ATGTTTAAAACAAGCCAAAATATTAAAAAAGTATGATCCAGTACGTAAAT
TTTCACGAAATTCAAATAAAGGTCACTTATTGAGTGACTAACATATGCCT
CATTAACCCTTTCACTGCGCAATATGTTTTGAGAGTTCATGTTCGATGTC
CGCAAATCTTTGATTATTGTACGTACAGATGCACAATCTTCCGATTTTAC
TATACTAAAAGTGAAACATCATCTTAGCATTTTTGTACCTGATTTGTTTG
AGTACTCTGTGTGAATAGTTGTGTTGAACCGGAATGAATTCGGAGCGTAT
TGGTCATTCATATTGTGCGAGTATATACGGCTTGAGCAGTGAAAGGGTTA
AATATTTATTTATATTATATTTTATATGAAATATCGAGTCATAACTATAA
AACATCCTTATTGGTAAATTTTTAATAAACCTTATCAGCATCAACT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000421tail