WormBase ParaSite HomeVersion: WBPS16 (WS279)
RNASeq Schmidtea mediterranea

Schmidtea mediterranea - public RNASeq studies

Table of Contents

Analysed

SRP009681: Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea

Genetics and Genome Sciences, University of Connecticut Health Center

Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. (Resch .. Graveley, 2012)

Design: 7 conditions

Condition num. replicates Cell type Strain Treatment
Asexual, Irradiated 1 Asexual Irradiated
Asexual, Non-irradiated 2 Asexual Non-irradiated
Sexual, Irradiated 1 Sexual Irradiated
Sexual, Non-irradiated 1 Sexual Non-irradiated
X1 neoblast, Sexual, Non-irradiated 1 X1 neoblast Sexual Non-irradiated
X2 neoblast, Sexual, Non-irradiated 1 X2 neoblast Sexual Non-irradiated
Xins differentiated cells, Sexual, Non-irradiated 1 Xins differentiated cells Sexual Non-irradiated

SRP013005: Planarian stem cell transcriptome

Pearson, Molecular Genetics, Hospital for Sick Children

Design: 3 conditions

Condition num. replicates Organism part
differentiated tissues 2 all tissues minus stem cells and progeny
stem cell progeny 2 stem cell progeny
stem cells 2 stem cells, neoblasts

SRP031467: Schmidtea mediterranea FoxD-GFP RNAi Differential Expression Analysis

SRP041596: Wound-induced neoblast specialization in S. mediterranea

Reddien Lab, Biology Department, Whitehead Institute, MIT

Neoblast specialization in regeneration of the planarian Schmidtea mediterranea. (Scimone .. Reddien, 2014)

Design: 3 conditions

Condition num. replicates Cell isolation method Cell type Strain Timepoint Treatment
0hr, control 3 FACS Isolated pre-pharyngeal X1 cells Asexual 0hr control
48hr, anterior wound 3 FACS Isolated pre-pharyngeal X1 cells Asexual 48hr anterior wound
48hr, posterior wound 3 FACS Isolated pre-pharyngeal X1 cells Asexual 48hr posterior wound

SRP062861: RNA Seq analysis of Schmidtea mediterranea treated with RNAi against chd4, p53, or unc22 to identify factors involved in neoblast differentiation.

Seidel, Genomics, Stowers Institute

Design: 17 conditions

Condition num. replicates RNAi Time after RNAi treatment Organism part
CHD4, 12 days 3 CHD4 12 days whole organism
CHD4, 15 days 3 CHD4 15 days whole organism
CHD4, 3 days 3 CHD4 3 days whole organism
CHD4, 6 days 3 CHD4 6 days whole organism
CHD4, 9 days 3 CHD4 9 days whole organism
p53, 12 days 3 p53 12 days whole organism
p53, 15 days 3 p53 15 days whole organism
p53, 18 days 2 p53 18 days whole organism
p53, 3 days 3 p53 3 days whole organism
p53, 6 days 3 p53 6 days whole organism
p53, 9 days 3 p53 9 days whole organism
unc22, 12 days 3 unc22 12 days whole organism
unc22, 15 days 3 unc22 15 days whole organism
unc22, 18 days 3 unc22 18 days whole organism
unc22, 3 days 3 unc22 3 days whole organism
unc22, 6 days 3 unc22 6 days whole organism
unc22, 9 days 3 unc22 9 days whole organism

SRP063836: RNA Seq analysis of sorted Schmidtea mediterranea X1 and Xins cells to identify factors specific to neoblasts

Wills Lab, Biochemistry, University of Washington

SRP064425: Planarian yorkie/YAP functions to integrate adult stem cell proliferation, organ homeostasis, and maintenance of axial patterning

Pearson, Molecular Genetics, Hospital for Sick Children

Planarian yorkie/YAP functions to integrate adult stem cell proliferation, organ homeostasis and maintenance of axial patterning. (Lin .. Pearson, 2014)

Design: 2 conditions

Condition num. replicates Organism part RNAi Strain
unc22 (control) 3 whole animal, mascerated unc22 (control) Asexual CIW4
yorkie 3 whole animal, mascerated yorkie Asexual CIW4

SRP064848: Set1 and MLL1/2 target distinct sets of functionally different genomic loci in vivo: An in depth RNA-seq analysis of H3K4me3 targets in vivo and upon Set1 and mll1 knockdown

Wills Lab, Biochemistry, University of Washington

Design: 14 conditions

Condition num. replicates Cell type Organism part RNAi Timepoint
X1, mll1/2, 12 days 4 X1 mll1/2 12 days
X1, mll1/2, 9 days 4 X1 mll1/2 9 days
X1, set1, 6 days 4 X1 set1 6 days
X1, set1, 9 days 4 X1 set1 9 days
X1, unc22, 12 days 4 X1 unc22 12 days
X1, unc22, 6 days 4 X1 unc22 6 days
X1, unc22, 9 days 8 X1 unc22 9 days
whole organism, mll1/2, 12 days 4 whole organism mll1/2 12 days
whole organism, mll1/2, 9 days 4 whole organism mll1/2 9 days
whole organism, set1, 6 days 4 whole organism set1 6 days
whole organism, set1, 9 days 4 whole organism set1 9 days
whole organism, unc22, 12 days 4 whole organism unc22 12 days
whole organism, unc22, 6 days 4 whole organism unc22 6 days
whole organism, unc22, 9 days 8 whole organism unc22 9 days

SRP066867: Conserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians (dataset 3)

Systems Biology Unit, Centre for Genomic Regulation

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. (Solana .. Rajewsky, 2016)

Design: 21 conditions

Condition num. replicates Cellular fraction Experiment Strain
Whole worm treated with dsRNA against Celf genes 1 Whole worm Celf siRNA Berlin-1 strain asexual type
Whole worm treated with dsRNA against Esrp genes 1 Whole worm Esrp siRNA Berlin-1 strain asexual type
Whole worm treated with dsRNA against GFP 1 Whole worm Control (GFP siRNA) Berlin-1 strain asexual type
Whole worm treated with dsRNA against Mbnl genes 1 Whole worm Mbnl siRNA Berlin-1 strain asexual type
Whole worm treated with dsRNA against Nova genes 1 Whole worm Nova siRNA Berlin-1 strain asexual type
Whole worm treated with dsRNA against Ptbp genes 1 Whole worm Ptbp siRNA Berlin-1 strain asexual type
Whole worm treated with dsRNA against Rbfox genes 1 Whole worm RbfoxS siRNA Berlin-1 strain asexual type
Whole worm treated with dsRNA against Rbfox1 1 Whole worm Rbfox1 siRNA Berlin-1 strain asexual type
Whole worm treated with dsRNA against bruli 1 Whole worm Bruli siRNA Berlin-1 strain asexual type
X1 fraction from Mbnl knocked down worms 2 X1 cell fraction Mbnl siRNA Berlin-1 strain asexual type
X1 fraction from bruli knocked down worms 2 X1 cell fraction Bruli siRNA Berlin-1 strain asexual type
X1 fraction from control worms 2 X1 cell fraction Control (GFP siRNA) Berlin-1 strain asexual type
X1 fraction from wild type worms 1 X1 cell fraction Wild type Berlin-1 strain asexual type
X2 fraction from Mbnl knocked down worms 1 X2 cell fraction Mbnl siRNA Berlin-1 strain asexual type
X2 fraction from bruli knocked down worms 1 X2 cell fraction Bruli siRNA Berlin-1 strain asexual type
X2 fraction from control worms 1 X2 cell fraction Control (GFP siRNA) Berlin-1 strain asexual type
X2 fraction from wild type worms 1 X2 cell fraction Wild type Berlin-1 strain asexual type
Xins fraction from Mbnl knocked down worms 2 Xins cell fraction Mbnl siRNA Berlin-1 strain asexual type
Xins fraction from bruli knocked down worms 2 Xins cell fraction Bruli siRNA Berlin-1 strain asexual type
Xins fraction from control worms 2 Xins cell fraction Control (GFP siRNA) Berlin-1 strain asexual type
Xins fraction from wild type worms 2 Xins cell fraction Wild type Berlin-1 strain asexual type

SRP071204: HOX gene complement and expression in the planarian Schmidtea mediterranea

Pearson, Molecular Genetics, Hospital for Sick Children

HOX gene complement and expression in the planarian Schmidtea mediterranea. (Currie .. Pearson, 2016)

Design: 6 conditions

Condition num. replicates Plane of amputation Strain Treatment
Wildtype zone 1 2 posterior extent of the photoreceptors Asexual CIW4 Amputation fragment
Wildtype zone 2 2 posterior extent of the brain Asexual CIW4 Amputation fragment
Wildtype zone 3 2 anterior extent of the pharynx Asexual CIW4 Amputation fragment
Wildtype zone 4 2 posterior extent of the pharynx Asexual CIW4 Amputation fragment
Wildtype zone 5 2 midpoint between posterior pharynx and tail tip Asexual CIW4 Amputation fragment
Wildtype zone 6 2 last remaining piece of tail tip Asexual CIW4 Amputation fragment

SRP073670: RNA Seq analysis of gene expression in Planaria at 24, 48, 72, and 96 hours after exposure to 6k rad of gamma irradiation.

Seidel, Genomics, Stowers Institute

Design: 5 conditions

Condition num. replicates Timepoint Treatment
0 hours 3 0 hours
24 hours, 6000 rads 3 24 hours 6000 rads
48 hours, 6000 rads 3 48 hours 6000 rads
72 hours, 6000 rads 3 72 hours 6000 rads
96 hours, 6000 rads 3 96 hours 6000 rads

SRP073671: RNA Seq analysis of neoblasts from Schmidtea mediterranea treated with RNAi against zfp1, p53, or unc22 to identify factors involved in neoblast differentiation.

SRP073672: RNA Seq analysis in flatworm following 6, 12, or 18 day treatment with RNAi against Pax5, Sox8, or Zfp1, relative to unc22 to identify transcriptional targets.

Seidel, Genomics, Stowers Institute

Design: 12 conditions

Condition num. replicates Organism part RNAi Timepoint
pax5, 12 days 4 whole_organism pax5 12 days
pax5, 18 days 4 whole_organism pax5 18 days
pax5, 6 days 4 whole_organism pax5 6 days
sox8, 12 days 4 whole_organism sox8 12 days
sox8, 18 days 4 whole_organism sox8 18 days
sox8, 6 days 4 whole_organism sox8 6 days
unc22, 12 days 4 whole_organism unc22 12 days
unc22, 18 days 4 whole_organism unc22 18 days
unc22, 6 days 4 whole_organism unc22 6 days
zfp1, 12 days 4 whole_organism zfp1 12 days
zfp1, 18 days 4 whole_organism zfp1 18 days
zfp1, 6 days 4 whole_organism zfp1 6 days

SRP074139: Schmidtea mediterranea isolate:CIW4 Raw sequence reads

University of Illinois at Urbana-Champaign

Design: 5 conditions

Condition num. replicates Organism part Strain Timepoint Treatment
12h regenerate 3 tail CIW4 12h postpharyngeal cut
36h regenerate 3 tail CIW4 36h postpharyngeal cut
72h regenerate 3 tail CIW4 72h postpharyngeal cut
Cut control 3 tail CIW4 postpharyngeal cut
Whole control 3 whole organism CIW4

SRP074285: Gene expression profiling of planarian heads or cephalic ganglia after inhibition of Hedgehog signaling pathway genes by RNAi

Whitehead Institute for Biomedical Research

Hedgehog signaling regulates gene expression in planarian glia. (Wang .. Reddien, 2016)

Design: 4 conditions

Condition num. replicates Organism part RNAi Strain
cephalic ganglia, hedgehog, S2F1L3F2 2 cephalic ganglia hedgehog S2F1L3F2
cephalic ganglia, patched, S2F1L3F2 2 cephalic ganglia patched S2F1L3F2
cephalic ganglia, unc-22, S2F1L3F2 2 cephalic ganglia unc-22 S2F1L3F2
head fragment, unc-22, CIW4 2 head fragment unc-22 CIW4

SRP074326: Schmidtea mediterranea Raw sequence reads (sexual strain and CPEB knockdowns)

Wright State University

Design: 3 conditions

Condition num. replicates Geographic location Isolation source Organism part RNAi Strain
CPEB1 3 Spain Newmark Laboratory (Illinois) whole organism CPEB1 sexual
CPEB2 3 Spain Newmark Laboratory (Illinois) whole organism CPEB2 sexual
control 3 Spain Newmark Laboratory (Illinois) whole organism sexual

SRP076161: RNA Seq analysis of gene expression during Schmidtea mediterranea embryogenesis, including yolk and adult samples

Seidel, Genomics, Stowers Institute

Embryonic origin of adult stem cells required for tissue homeostasis and regeneration. (Davies .. Alvarado, 2017)

Design: 10 conditions

Condition num. replicates Biotype Day Developmental stage
asexual, asexual CIW4 adult 4 asexual asexual CIW4 adult
sexual, 10, Stage 7 embryo 4 sexual 10 Stage 7 embryo
sexual, 14, Stage 8 embryo 4 sexual 14 Stage 8 embryo
sexual, 2, Stage 2 embryo 4 sexual 2 Stage 2 embryo
sexual, 3, Stage 3 embryo 4 sexual 3 Stage 3 embryo
sexual, 4, Stage 4 embryo 4 sexual 4 Stage 4 embryo
sexual, 6, Stage 5 embryo 4 sexual 6 Stage 5 embryo
sexual, 9, Stage 6 embryo 4 sexual 9 Stage 6 embryo
sexual, Yolk 4 sexual Yolk
sexual, virgin, sexuallly mature adult 4 sexual virgin, sexuallly mature adult

SRP077922: Egf signaling directs neoblast repopulation by regulating asymmetric cell division in planarians

Seidel, Genomics, Stowers Institute

Egf Signaling Directs Neoblast Repopulation by Regulating Asymmetric Cell Division in Planarians. (Lei .. Sánchez Alvarado, 2016)

Design: 36 conditions

Condition num. replicates Organism part RNAi Strain Timepoint
whole organism, Egfr3 3 feedings NT, 9 days 4 whole organism Egfr3 3 feedings NT asexual CIW4 9 days
whole organism, Egfr3 6 feedings SR, 22 days 4 whole organism Egfr3 6 feedings SR asexual CIW4 22 days
whole organism, Egfr3 6 feedings SR, 23 days 4 whole organism Egfr3 6 feedings SR asexual CIW4 23 days
whole organism, Egfr3 6 feedings SR, 26 days 4 whole organism Egfr3 6 feedings SR asexual CIW4 26 days
whole organism, Egfr3 6 feedings SR, 28 days 4 whole organism Egfr3 6 feedings SR asexual CIW4 28 days
whole organism, Egfr3 6 feedings SR, 30 days 4 whole organism Egfr3 6 feedings SR asexual CIW4 30 days
whole organism, Egfr3 6 feedings SR, 32 days 4 whole organism Egfr3 6 feedings SR asexual CIW4 32 days
whole organism, Egfr3 8 feedings NT, 30 days 4 whole organism Egfr3 8 feedings NT asexual CIW4 30 days
whole organism, Unc22 3 feedings NT, 9 days 4 whole organism Unc22 3 feedings NT asexual CIW4 9 days
whole organism, Unc22 6 feedings SR, 22 days 4 whole organism Unc22 6 feedings SR asexual CIW4 22 days
whole organism, Unc22 6 feedings SR, 23 days 4 whole organism Unc22 6 feedings SR asexual CIW4 23 days
whole organism, Unc22 6 feedings SR, 26 days 4 whole organism Unc22 6 feedings SR asexual CIW4 26 days
whole organism, Unc22 6 feedings SR, 28 days 4 whole organism Unc22 6 feedings SR asexual CIW4 28 days
whole organism, Unc22 6 feedings SR, 30 days 4 whole organism Unc22 6 feedings SR asexual CIW4 30 days
whole organism, Unc22 6 feedings SR, 32 days 4 whole organism Unc22 6 feedings SR asexual CIW4 32 days
whole organism, Unc22 8 feedings NT, 30 days 4 whole organism Unc22 8 feedings NT asexual CIW4 30 days
whole organism, nrg6 3 feedings NT, 9 days 4 whole organism nrg6 3 feedings NT asexual CIW4 9 days
whole organism, nrg6 6 feedings SR, 22 days 4 whole organism nrg6 6 feedings SR asexual CIW4 22 days
whole organism, nrg6 6 feedings SR, 23 days 4 whole organism nrg6 6 feedings SR asexual CIW4 23 days
whole organism, nrg6 6 feedings SR, 26 days 4 whole organism nrg6 6 feedings SR asexual CIW4 26 days
whole organism, nrg6 6 feedings SR, 28 days 4 whole organism nrg6 6 feedings SR asexual CIW4 28 days
whole organism, nrg6 6 feedings SR, 30 days 4 whole organism nrg6 6 feedings SR asexual CIW4 30 days
whole organism, nrg6 6 feedings SR, 32 days 4 whole organism nrg6 6 feedings SR asexual CIW4 32 days
whole organism, nrg6 8 feedings NT, 30 days 4 whole organism nrg6 8 feedings NT asexual CIW4 30 days
whole organism, nrg7 3 feedings NT, 9 days 4 whole organism nrg7 3 feedings NT asexual CIW4 9 days
whole organism, nrg7 6 feedings SR, 22 days 4 whole organism nrg7 6 feedings SR asexual CIW4 22 days
whole organism, nrg7 6 feedings SR, 23 days 4 whole organism nrg7 6 feedings SR asexual CIW4 23 days
whole organism, nrg7 6 feedings SR, 26 days 4 whole organism nrg7 6 feedings SR asexual CIW4 26 days
whole organism, nrg7 6 feedings SR, 28 days 4 whole organism nrg7 6 feedings SR asexual CIW4 28 days
whole organism, nrg7 6 feedings SR, 30 days 4 whole organism nrg7 6 feedings SR asexual CIW4 30 days
whole organism, nrg7 6 feedings SR, 32 days 4 whole organism nrg7 6 feedings SR asexual CIW4 32 days
whole organism, nrg7 8 feedings NT, 30 days 4 whole organism nrg7 8 feedings NT asexual CIW4 30 days
x1, Egfr3 8 feedings NT, 30 days 4 x1 Egfr3 8 feedings NT asexual CIW4 30 days
x1, Unc22 8 feedings NT, 30 days 4 x1 Unc22 8 feedings NT asexual CIW4 30 days
x1, nrg6 8 feedings NT, 30 days 4 x1 nrg6 8 feedings NT asexual CIW4 30 days
x1, nrg7 8 feedings NT, 30 days 4 x1 nrg7 8 feedings NT asexual CIW4 30 days

SRP091669: NPY-8-internalizing cells transcriptome in Schmidtea mediterranea

University of Illinois at Urbana-Champaign

Design: 2 conditions

Condition num. replicates Organism part Developmental stage Strain
control dissociated cells 4 control dissociated cells Mature Sexual
npy-8-internalizing dissociated cells 4 npy-8-internalizing dissociated cells Mature Sexual

SRP103921: Yorkie is required to restrict the injury responses in planarians

Pearson, Molecular Genetics, Hospital for Sick Children

Yorkie is required to restrict the injury responses in planarians. (Lin .. Pearson, 2017)

Design: 4 conditions

Condition num. replicates Organism part Strain Treatment
tail, Control RNAi 9 tail Asexual CIW4 Control RNAi
tail, Yki RNAi 9 tail Asexual CIW4 Yki RNAi
whole organism, Control RNAi 3 whole organism Asexual CIW4 Control RNAi
whole organism, Yki RNAi 3 whole organism Asexual CIW4 Yki RNAi

SRP107206: Gene expression profiling of intact individual planarians during homeostatic tissue turnover after inhibition of myoD or nkx1-1

Whitehead Institute for Biomedical Research

Orthogonal muscle fibres have different instructive roles in planarian regeneration. (Scimone .. Reddien, 2017)

Design: 4 conditions

Condition num. replicates Organism part RNAi RNAi feedings Strain
myoD, 10 6 whole organism myoD 10 CIW4
nkx1-1, 12 7 whole organism nkx1-1 12 CIW4
unc-22 (control), 10 6 whole organism unc-22 (control) 10 CIW4
unc-22 (control), 12 5 whole organism unc-22 (control) 12 CIW4

SRP107207: Gene expression profiling of regenerating planarian tails after inhibition of myoD and follistatin

Whitehead Institute for Biomedical Research

Orthogonal muscle fibres have different instructive roles in planarian regeneration. (Scimone .. Reddien, 2017)

Design: 4 conditions

Condition num. replicates Organism part RNAi RNAi feedings Strain
fst, 6 12 tail fragment fst 6 CIW4
myoD, 10 12 tail fragment myoD 10 CIW4
unc-22 (control), 10 12 tail fragment unc-22 (control) 10 CIW4
unc-22 (control), 6 12 tail fragment unc-22 (control) 6 CIW4

SRP115085: The planarian TCF/LEF factor Smed-tcf1 is required for the regeneration of dorsal-lateral neuronal subtypes

Pearson, Molecular Genetics, Hospital for Sick Children

The planarian TCF/LEF factor Smed-tcf1 is required for the regeneration of dorsal-lateral neuronal subtypes. (Brown .. Pearson, 2018)

Design: 18 conditions

Condition num. replicates Organism part Strain Timepoint Treatment
1 days, APC RNAi 1 regenerating trunk fragments Asexual CIW4 1 days APC RNAi
1 days, Bcat RNAi 1 regenerating trunk fragments Asexual CIW4 1 days Bcat RNAi
1 days, Control RNAi 1 regenerating trunk fragments Asexual CIW4 1 days Control RNAi
2 days, APC RNAi 1 regenerating trunk fragments Asexual CIW4 2 days APC RNAi
2 days, Bcat RNAi 1 regenerating trunk fragments Asexual CIW4 2 days Bcat RNAi
2 days, Control RNAi 1 regenerating trunk fragments Asexual CIW4 2 days Control RNAi
3 days, APC RNAi 1 regenerating trunk fragments Asexual CIW4 3 days APC RNAi
3 days, Bcat RNAi 1 regenerating trunk fragments Asexual CIW4 3 days Bcat RNAi
3 days, Control RNAi 1 regenerating trunk fragments Asexual CIW4 3 days Control RNAi
4 days, APC RNAi 1 regenerating trunk fragments Asexual CIW4 4 days APC RNAi
4 days, Bcat RNAi 1 regenerating trunk fragments Asexual CIW4 4 days Bcat RNAi
4 days, Control RNAi 1 regenerating trunk fragments Asexual CIW4 4 days Control RNAi
5 days, APC RNAi 1 regenerating trunk fragments Asexual CIW4 5 days APC RNAi
5 days, Bcat RNAi 1 regenerating trunk fragments Asexual CIW4 5 days Bcat RNAi
5 days, Control RNAi 1 regenerating trunk fragments Asexual CIW4 5 days Control RNAi
6 days, APC RNAi 1 regenerating trunk fragments Asexual CIW4 6 days APC RNAi
6 days, Bcat RNAi 1 regenerating trunk fragments Asexual CIW4 6 days Bcat RNAi
6 days, Control RNAi 1 regenerating trunk fragments Asexual CIW4 6 days Control RNAi

SRP115287: Schmidtea mediterranea Integrator complex subunit knockdown and small RNA sequencing

Max Planck Institute for Molecular Biomedicine

Cells-in-Motion Cluster of Excellence
Max Planck Institute for Molecular Biomedicine
Stem cells and Regeneration Group

Design: 3 conditions

Condition num. replicates Developmental stage Isolate Organism part Strain Treatment
x1 cells 3 adult BCN-10 x1 cells asexual
x1 cells, ints3 RNAi 3 adult BCN-10 x1 cells asexual ints3 RNAi
x1 cells, ints9 RNAi 3 adult BCN-10 x1 cells asexual ints9 RNAi

SRP126428: A tetraspanin family member functionally resolves and facilitates the purification of adult pluripotent stem cells used for whole-body regeneration (Bulk)

Stowers Institute for Medical Research

Prospectively Isolated Tetraspanin+ Neoblasts Are Adult Pluripotent Stem Cells Underlying Planaria Regeneration. (Zeng .. Sánchez Alvarado, 2018)

Design: 25 conditions

Condition num. replicates Cell type Genotype Irradiation Organism part Timepoint Treatment
24hours after 10K irradiation, whole organism 3 wild type 24hours after 10K irradiation whole organism
sorted piwi-1 high cells 4 sorted piwi-1 high cells wild type
sorted piwi-1 low cells 4 sorted piwi-1 low cells wild type
sorted piwi-1 negative cells 4 sorted piwi-1 negative cells wild type
sorted x1 cells 3 sorted x1 cells wild type
sorted x2 cells 3 sorted x2 cells wild type
sorted xins cells 3 sorted xins cells wild type
whole organism 3 wild type whole organism
whole organism, 0hr, amputation 4 wild type whole organism 0hr amputation
whole organism, 10day, amputation 4 wild type whole organism 10day amputation
whole organism, 12hr, amputation 4 wild type whole organism 12hr amputation
whole organism, 14day, amputation 4 wild type whole organism 14day amputation
whole organism, 1hr, amputation 4 wild type whole organism 1hr amputation
whole organism, 24hr, amputation 4 wild type whole organism 24hr amputation
whole organism, 36hr, amputation 4 wild type whole organism 36hr amputation
whole organism, 3hr, amputation 4 wild type whole organism 3hr amputation
whole organism, 48hr, amputation 4 wild type whole organism 48hr amputation
whole organism, 4day, amputation 4 wild type whole organism 4day amputation
whole organism, 5day, amputation 4 wild type whole organism 5day amputation
whole organism, 60hr, amputation 4 wild type whole organism 60hr amputation
whole organism, 6day, amputation 4 wild type whole organism 6day amputation
whole organism, 6hr, amputation 4 wild type whole organism 6hr amputation
whole organism, 72hr, amputation 4 wild type whole organism 72hr amputation
whole organism, 7day, amputation 4 wild type whole organism 7day amputation
whole organism, 9hr, amputation 4 wild type whole organism 9hr amputation

SRP126458: Sexual Regeneration RNAseq

Sanchez Alvarado Lab, Stowers Institute for Medical Research

Design: 5 conditions

Condition num. replicates Organism part Strain Timepoint
trunk fragments, day 0 3 trunk fragments Sexual S2F2 day 0
trunk fragments, day 3 3 trunk fragments Sexual S2F2 day 3
trunk fragments, day 5 3 trunk fragments Sexual S2F2 day 5
trunk fragments, day 7 3 trunk fragments Sexual S2F2 day 7
whole juvenile animal 3 whole organism Sexual S2F2

SRP158184: Smed-myb-1 specifies early temporal identity during planarian epidermal differentiation

Pearson, Molecular Genetics, Hospital for Sick Children

Smed-myb-1 Specifies Early Temporal Identity during Planarian Epidermal Differentiation. (Zhu .. Pearson, 2018)

Design: 6 conditions

Condition num. replicates Source name Strain Treatment
Asexual CIW10, myb-1 RNAi 2 Wildtype animals (30 animals) Asexual CIW10 myb-1 RNAi
Asexual CIW12, myb-1 RNAi 2 Wildtype animals (30 animals) Asexual CIW12 myb-1 RNAi
Asexual CIW14, myb-1 RNAi 2 Wildtype animals (30 animals) Asexual CIW14 myb-1 RNAi
Asexual CIW4, control RNAi 2 Wildtype animals (30 animals) Asexual CIW4 control RNAi
Asexual CIW6, control RNAi 2 Wildtype animals (30 animals) Asexual CIW6 control RNAi
Asexual CIW8, control RNAi 2 Wildtype animals (30 animals) Asexual CIW8 control RNAi

SRP164884: RNA sequencing of pole-containing anterior tip regions in planarian Schmidtea mediterranea

Whitehead Institute for Biomedical Research

Nuclear receptor NR4A is required for patterning at the ends of the planarian anterior-posterior axis. (Li .. Reddien, 2019)

Design: 4 conditions

Condition num. replicates Organism part Treatment Ploidy Strain
non-pole-containing anterior blastema flanking region 3 non-pole-containing anterior blastema flanking region 72-hours-post transverse amputation 2N (non-dividing) asexual CIW4
non-pole-containing head tip flanking region 3 non-pole-containing head tip flanking region 2N (non-dividing) asexual CIW4
pole-containing anterior blastema region 3 pole-containing anterior blastema region 72-hours-post transverse amputation 2N (non-dividing) asexual CIW4
pole-containing head tip region 3 pole-containing head tip region 2N (non-dividing) asexual CIW4

SRP164885: RNA sequencing of the head and tail of planarian Schmidtea mediterranea during nr4A inhibition

Whitehead Institute for Biomedical Research

Nuclear receptor NR4A is required for patterning at the ends of the planarian anterior-posterior axis. (Li .. Reddien, 2019)

Design: 16 conditions

Condition num. replicates Organism part Timepoint Treatment Ploidy Strain
head, 2 weeks 3 head 2 weeks 2N (non-dividing) asexual CIW4
head, 2 weeks, nr4A 3 head 2 weeks nr4A 2N (non-dividing) asexual CIW4
head, 3 weeks 3 head 3 weeks 2N (non-dividing) asexual CIW4
head, 3 weeks, nr4A 3 head 3 weeks nr4A 2N (non-dividing) asexual CIW4
head, 4 weeks 3 head 4 weeks 2N (non-dividing) asexual CIW4
head, 4 weeks, nr4A 3 head 4 weeks nr4A 2N (non-dividing) asexual CIW4
head, 5 weeks 3 head 5 weeks 2N (non-dividing) asexual CIW4
head, 5 weeks, nr4A 3 head 5 weeks nr4A 2N (non-dividing) asexual CIW4
tail, 2 weeks 3 tail 2 weeks 2N (non-dividing) asexual CIW4
tail, 2 weeks, nr4A 3 tail 2 weeks nr4A 2N (non-dividing) asexual CIW4
tail, 3 weeks 3 tail 3 weeks 2N (non-dividing) asexual CIW4
tail, 3 weeks, nr4A 3 tail 3 weeks nr4A 2N (non-dividing) asexual CIW4
tail, 4 weeks 3 tail 4 weeks 2N (non-dividing) asexual CIW4
tail, 4 weeks, nr4A 3 tail 4 weeks nr4A 2N (non-dividing) asexual CIW4
tail, 5 weeks 3 tail 5 weeks 2N (non-dividing) asexual CIW4
tail, 5 weeks, nr4A 3 tail 5 weeks nr4A 2N (non-dividing) asexual CIW4

SRP167900: Planarians recruit piRNAs for mRNA turnover in adult stem cells

BIOmac Research Center, NW I, University of Bayreuth

Design: 8 conditions

Condition num. replicates RNAi Tissue Strain
X1 cells 3 FACS-sorted neoblasts (X1 cells) CIW4
X1 cells, smedwi-2 RNAi 3 Smedwi-2 RNAi FACS-sorted neoblasts (X1 cells) CIW4
X1 cells, smedwi-3 RNAi 3 smedwi-3 RNAi FACS-sorted neoblasts (X1 cells) CIW4
X1 cells, unc-22 RNAI 6 Unc-22 RNAi (control) FACS-sorted neoblasts (X1 cells) CIW4
Xins cells, smedwi-2 RNAi 3 Smedwi-2 RNAi FACS-sorted differentiated cells (Xins cells) CIW4
Xins cells, smedwi-3 RNAi 3 smedwi-3 RNAi FACS-sorted differentiated cells (Xins cells) CIW4
Xins cells, unc-22 RNAi 6 Unc-22 RNAi (control) FACS-sorted differentiated cells (Xins cells) CIW4
whole worm 2 whole worm CIW4

SRP181555: Transcriptomic analysis of planarians under simulated microgravity and hypergravity

Universitat de Barcelona

Design: 8 conditions

Condition num. replicates Regeneration days Gravity Developmental stage Molecule Organism part Sex Strain
hypergravity control, 12 days 2 12 hypergravity control adult polyA RNA whole organism asexual asexual BCN-10 clonal line
hypergravity control, 5 days 2 5 hypergravity control adult polyA RNA whole organism asexual asexual BCN-10 clonal line
hypergravity test, 12 days 2 12 hypergravity test adult polyA RNA whole organism asexual asexual BCN-10 clonal line
hypergravity test, 5 days 2 5 hypergravity test adult polyA RNA whole organism asexual asexual BCN-10 clonal line
microgravity control, 12 days 2 12 microgravity control adult polyA RNA whole organism asexual asexual BCN-10 clonal line
microgravity control, 5 days 2 5 microgravity control adult polyA RNA whole organism asexual asexual BCN-10 clonal line
microgravity test, 12 days 2 12 microgravity test adult polyA RNA whole organism asexual asexual BCN-10 clonal line
microgravity test, 5 days 2 5 microgravity test adult polyA RNA whole organism asexual asexual BCN-10 clonal line

SRP214683: Tnfaip2/Exoc3 driven lipid metabolism is essential for stem cell differentiation & organ homeostasis [Schmidtea mediterranea]

Core Facility Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute

Tnfaip2/exoc3-driven lipid metabolism is essential for stem cell differentiation and organ homeostasis. (Deb .. Rudolph, 2021)

Design: 2 conditions

Condition num. replicates Depletion Cell cycle Irradiation sensitivity Source name
Smed-exoc3 3 Smed-exoc3 mitotically active irradiation sensitive X1
gfp (control) 3 gfp (control) mitotically active irradiation sensitive X1

SRP217572: Conserved targets of Wnt signaling in Schmidtea mediterranea and Hofstenia miamia

Whitehead Institute for Biomedical Research

Design: 17 conditions

Condition num. replicates Irradiation RNAi condition Time Organism part Strain
bcat RNAi, day 1 1 no bcat RNAi day 1 tail asexual CIW4
bcat RNAi, day 2 1 no bcat RNAi day 2 tail asexual CIW4
bcat RNAi, day 4 2 no bcat RNAi day 4 tail asexual CIW4
bcat RNAi, day 4, irradiated 1 yes bcat RNAi day 4 tail asexual CIW4
bcat RNAi, day 6 1 no bcat RNAi day 6 tail asexual CIW4
sp5 RNAi, 1 week 1 no sp5 RNAi 1 week tail asexual CIW4
sp5 RNAi, 2 weeks 1 no sp5 RNAi 2 weeks tail asexual CIW4
sp5 RNAi, 4 weeks 1 no sp5 RNAi 4 weeks tail asexual CIW4
unc RNAi, 1 week 1 no unc RNAi 1 week tail asexual CIW4
unc RNAi, 2 weeks 1 no unc RNAi 2 weeks tail asexual CIW4
unc RNAi, 4 weeks 1 no unc RNAi 4 weeks tail asexual CIW4
unc RNAi, day 0 1 no unc RNAi day 0 tail asexual CIW4
unc RNAi, day 1 1 no unc RNAi day 1 tail asexual CIW4
unc RNAi, day 2 1 no unc RNAi day 2 tail asexual CIW4
unc RNAi, day 4 2 no unc RNAi day 4 tail asexual CIW4
unc RNAi, day 4, irradiated 1 yes unc RNAi day 4 tail asexual CIW4
unc RNAi, day 6 1 no unc RNAi day 6 tail asexual CIW4

SRP255875: Gene expression profiling for: activin-2 is required for regeneration of polarity on the planarian anterior-posterior axis

MIT Biology, Whitehead Institute for Biomedical Research

Design: 6 conditions

Condition num. replicates RNAi Wound orientation Organism part RNAi feedings Strain
activin-2 RNAi 6 activin-2 post pharyngeal fragment 4F CIW4
anterior-facing wound, activin-2 RNAi 4 activin-2 anterior-facing wound post pharyngeal fragment 4F CIW4
anterior-facing wound, unc-22 RNAi 4 unc-22 anterior-facing wound post pharyngeal fragment 4F CIW4
posterior-facing wound, activin-2 RNAi 22 activin-2 posterior-facing wound post pharyngeal fragment 4F CIW4
posterior-facing wound, unc-22 RNAi 21 unc-22 posterior-facing wound post pharyngeal fragment 4F CIW4
unc-22 RNAi 6 unc-22 post pharyngeal fragment 4F CIW4

Other

These studies are available in ENA, and the reads successfully align to our genomes.
They have not been included in our analysis for one of the following reasons:
Failed to meet minimal criteria for differential expression analysis, failure to pass data quality filters, or we were unable to interpret accompanying metadata.

ERP000581: The head-regeneration transcriptome of the planarian Schmidtea mediterranea

High Throughput Sequencing Unit at the Genomics & Proteomics Core Facility, German Cancer Research Center (DKFZ), Germany

The head-regeneration transcriptome of the planarian Schmidtea mediterranea. (Sandmann .. Bartscherer, 2011)
E-MTAB-607 in ArrayExpress

7 runs in ENA

SRP006000: De novo assembly and validation of Planaria transcriptome by massive parallel sequencing and shotgun proteomics

SRP026030: Schmidtea mediterranea Transcriptome or Gene expression

Max Planck Institute of Molecular Cell Biology and Genetics

Reactivating head regrowth in a regeneration-deficient planarian species. (Liu .. Rink, 2013)

8 runs in ENA

SRP028872: Schmidtea mediterranea S2F2 Genome sequencing

Stowers Institute for Medical Research

Schmidtea mediterreanea Database

1 run in ENA

SRP028969: Schmidtea mediterranea CIW4 Transcriptome

Stowers Institute for Medical Research

Schmidtea mediterranea database

2 runs in ENA

SRP035509: Schmidtea mediterranea strain:CIW4 Transcriptome or Gene expression

San Diego State University

6 runs in ENA

SRP042226: Schmidtea mediterranea strain:clone 4Transcriptome or Gene expression

Whitehead Institute

1 run in ENA

SRP043140: Schmidtea mediteranea RNAi knockdown (ß-catenin, notum vs GFP)

SRP043189: Schmidtea mediterranea Transcriptome Assembly

Max Planck Institute for Molecular Biomedicine

2 runs in ENA

SRP058017: A mex3 homolog is required for differentiation during planarian stem cell lineage development

Pearson, Molecular Genetics, Hospital for Sick Children

10 runs in ENA

SRP059140: Schmidtea mediterranea Raw sequence reads

The Whitehead Institute for Biomedical Research

719 runs in ENA

SRP065271: Single-muscle-cell transcriptome profiling along the planarian anteroposterior axis

SRP066558: Conserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians (dataset 1)

SRP070102: PolyA position Profiling (3P-Seq) in Schmidtea mediterranea

Institute for Stem cell biology and Regenerative medicine (inStem)

Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea. (Lakshmanan .. Palakodeti, 2016)

4 runs in ENA

SRP078739: Role of microRNA miR124c during planarian brain regeneration.

Institute for Stem cell biology and Regenerative medicine (inStem)

2 runs in ENA

SRP078776: Role of cytoplasmic poly (A) binding protein during planaria regeneration

Institute for Stem cell biology and Regenerative medicine (inStem)

4 runs in ENA

SRP083006: transcriptome of Smed-LPT RNAi

University of Oxford

4 runs in ENA

SRP093467: Planarian epidermal stem cells respond to positional cues to promote cell type diversity

The Whitehead Institute for Biomedical Research

14 runs in ENA

SRP095154: Gene expression profiles along the planarian A/P axis.

MPI-CBG

Rink lab web page

11 runs in ENA

SRP100443: Smed-hippo(RNAi) RNA-Seq

Single Cell Genomics, Development, Centro Nacional de Análisis Genómico

Hippo signaling controls cell cycle and restricts cell plasticity in planarians. (de Sousa .. Adell, 2018)

18 runs in ENA

SRP102921: Schmidtea mediterranea strain:S2 Genome sequencing and assembly

Max Planck Institute of Molecular Cell Biology and Genetics

The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms. (Grohme .. Rink, 2018)
Planmine

1 run in ENA

SRP109123: Schmidtea mediterranea cultivar:S2F2 Transcriptome or Gene expression

SRP113707: Schmidtea mediterranea sexual vs. asexual head sequence reads

Wright State University

6 runs in ENA

SRP121652: FOX and ETS family transcription factors regulate the pigment cell lineage in planarians

SRP126228: nhr1 RNAi

Sanchez Alvarado Lab, Stowers Institute for Medical Research

32 runs in ENA

SRP126427: Tetraspanin family member functionally resolves and facilitates the purification of adult pluripotent stem cells used for whole-body regeneration (Single)

SRP158958: Transcriptional profiling of soxB1-2 RNAi planarians

San Diego State University

18 runs in ENA

SRP161555: Gene expression profiling of planarians after inhibition of hmcn-1

SRP168467: A FoxF-1 regulatory program controls specification of muscle subsets and phagocytic cells in planarians

The Whitehead Institute for Biomedical Research

101 runs in ENA

SRP213858: Transcriptome of cct3A(RNAi) planarians at 72 hours of regeneration

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

6 runs in ENA

SRP214257: Transcriptional profile of planarian FACS populations at different nutritional status

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

36 runs in ENA

SRP217326: Transcriptional profiling of laser captured intestinal tissue from the planarian Schmidtea mediterranea

S-314, Genes and Human Disease Research Program, Oklahoma Medical Research Foundation

12 runs in ENA

SRP270347: RNA-Seq of adar1, adar2 and control RNAi worms (planarians)

Morgridge Institute for Research

20 runs in ENA

SRP272800: Mitochondrial state determines functionally divergent stem cell population in planaria

Institute for Stem cell science and Regenerative medicine (inStem)

12 runs in ENA

SRP285746: Canonical and early lineage-specific stem cell types identified in planarian SirNeoblasts

SRP288179: The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells

SRP303889: Schmidtea mediterranea 10X G1/G0 scRNA-seq

SRP310765: Examination of gene expression in S. mediterranea transitioning from recirculation to static culture in the presence or absence of Gentamycin at 0, 1, 2, 3, or 4 days