SMED30016721

Overview
NameSMED30016721
Smed IDSMED30016721
Length (bp)860
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 SMED30016721 (SMED30016721) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016721 (SMED30016721) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 SMED30016721 (SMED30016721) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016721 (SMED30016721) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top


 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30016721

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 cellSMED30016721SMESG000042777.1 SMESG000003342.1 SmedASXL_078049SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30016721SMESG000042777.1 SMESG000003342.1 SmedASXL_078049SmedAsxl_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
SMED30016721 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001614:40769..44567 +4091
v31.020712:6955..7913 +4054
v31.000110:219741..220699 +4048
v31.006148:21282..22240 +4000
v31.000432:61749..62698 -3909
v31.000866:47979..48960 +3897
v31.024503:2938..3887 -3873
v31.000425:109695..110645 -3863
v31.006673:3908..4884 +3855
v31.004142:23625..24559 -3838
v31.000270:129387..130363 -3830
v31.001290:44477..45455 +3816
v31.013379:1366..2344 -3807
v31.004140:1317..2277 +3779
v31.000634:53202..54180 +3773
v31.003047:16803..17763 -3759
v31.008909:4292..5260 -3755
v31.004710:21006..21954 -3739
v31.002089:29134..30109 -3728
v31.000305:58111..59080 -3713
v31.000148:169162..170135 +3696
v31.000126:179760..180724 +3683
v31.000233:108796..109766 -3658
v31.004646:15767..16742 +3646
v31.004239:43323..44301 +3641
v31.006244:26656..27601 +3638
v31.000107:190366..191339 +3635
v31.000170:164694..165621 -3594
v31.005904:23428..24398 -3583
v31.007859:11975..12912 -3558
v31.012766:3001..3941 -3546
v31.000919:67005..67952 -3393
v31.002656:7992..8924 -3384
v31.004848:16806..17756 -3383
v31.003619:13180..14105 -3242
v31.000550:31866..32802 +3214
v31.010554:4343..5281 -3182
v31.000017:78210..79138 +3160
v31.004405:46500..47449 +3157
v31.006560:5313..6243 -3142
v31.000574:17218..18149 +3124
v31.014925:11652..12597 +3118
v31.008261:22337..23274 +3102
v31.000064:234473..235364 -3097
v31.001561:23400..24311 -3065
v31.009610:10733..11637 +3059
v31.000536:108121..109052 +3053
v31.000889:42615..43535 +3024
v31.000226:57444..58374 +3019
v31.006925:1357..2280 -2963
v31.015452:2671..3594 -2947
v31.001097:84595..85492 -2805
v31.003003:31657..32557 -2771
v31.000426:21733..22612 +2719
v31.018151:7779..8670 +2560
v31.001632:6700..7456 +2548
v31.000768:10455..11349 -2488
v31.002124:93942..94794 -2424
v31.000941:55406..56296 -2343
v31.000709:74304..75199 +2337
v31.034167:3826..4717 +2304
v31.001285:61431..62331 -2248
Homology
The following BLAST results are available for this feature:
BLAST of SMED30016721 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016721 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016721 ID=SMED30016721|Name=SMED30016721|organism=Schmidtea mediterranea sexual|type=transcript|length=860bp
ATTTTCTCCTGGGTCGTTTGGTGAATTCATAACTTTCAGCTAGGTTAGAA
TGATGTATTTCTTCTGACGTCGGTTAATATATTGGTTGAGTGTGCGTGTT
ATGTGCCGGATGATCCGGGTAGGTAGACATGAATGAAATGTCAATTACAG
CGTGACAACAGCGAGGTGGATGTTTATATTGGTTGATCGGCGGAAATGTC
GGCGAGCTTTATTAAGGTAAAATTGTTTATTTCATGGATTGTAAATTTAT
GAAATTCAGTTTAGGCTAATTGTACTTTAGGATTGCGAGTTTTGTGAGTT
ATTTGGAATTTAGCGTGCAATGCGTGTGAATTCGGGGGATCAGTTCACCC
TGTCATTTCGCGGGAGTTGCATATTTCCTTAGCGTTGACTATAACTGCGT
TTTGGATTGTCCCTATCTCTCGCTGCTGATCGCCCAGATGGTTTATCAGA
AAAGTTTGTTGATTTCTTAACTCTCTCTGGTCGCCTGGGAATTCTCCTCG
TTAAAAGTTTTCACAGCGGCAATTGCAGTTAGAAGTTGTTTGTCAGATCT
ATCTGTCTCCCTTTGGATATCACTGGCTGTGTGTGATTTACTCAGTGAAG
TCTCTATTCAGATTTTCTTTGCAATTTGGTATTATTATTCGTTATCAATC
ACGACAAGGAAAAATTGTTCTGGGTATGATGGAACTCTAGTCTAGCCGAA
CCTTCAACAAAATCGGATTGCTACGCTCGTCGTCTGGGCTTTGTCTTATA
GTCCTAACTCTATCATTTCGGTGTGAATTTAATGGAATCTTGACGATATC
TTATGCCTATGCGTGGTGAAGTTGATTTTGGTAAGTTAAAATAAAGTTTA
AGCGTCTTTA
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell