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RNASeq Macrostomum lignano

Macrostomum lignano - public RNASeq studies

Analysed

SRP082513: Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano

University Medical Center Groningen

Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano. (Grudniewska .. Berezikov, 2016)

Design: 16 conditions

Condition num. replicates Cell type Developmental stage Organism part Sample name Strain Treatment
G1 stage adult, regenerating head 1 G1 cells adult regenerating head cells in G1 cell cycle stage from regenerating heads DV1
G1 stage adult, whole organism 1 G1 cells adult whole organism cells in G1 cell cycle stage from adult animals DV1
irradiation 210Gy, 0h 1 adult whole organism adult animals 0 hours after irradiation with the cumulative dose of 210Gy DV1 worms are irradiated with three pulses of 70Gy every 4 hours and collected after the last pulse
irradiation 210Gy, 12h 1 adult whole organism adult animals 12 hours after irradiation with the cumulative dose of 210Gy DV1 worms are irradiated with three pulses of 70Gy every 4 hours and collected 12h after the last pulse
irradiation 210Gy, 24h 1 adult whole organism adult animals 24 hours after irradiation with the cumulative dose of 210Gy DV1 worms are irradiated with three pulses of 70Gy every 4 hours, transferred to food and collected 24h after the last pulse (straved 12h prior collection)
irradiation 210Gy, 72h 1 adult whole organism adult animals 72 hours after irradiation with the cumulative dose of 210Gy DV1 worms are irradiated with three pulses of 70Gy every 4 hours, transferred to food and collected 72h after the last pulse (straved 12h prior collection)
juvenile 2 juvenile
late-S/G2/M stage adult, regenerating head 1 S/G2/M cells adult regenerating head cells in late-S/G2/M cell cycle stage from regenerating heads DV1
late-S/G2/M stage adult, whole organism 1 S/G2/M cells adult whole organism cells in late-S/G2/M cell cycle stage from adult animals DV1
low salinity, 15h 1 mixed population whole organism mixed population at low salinity for 15 hours DV1 worms are kept at 1.5? salinity for 15h
low salinity, 1h 1 mixed population whole organism mixed population at low salinity for 1 hour DV1 worms are kept at 1.5? salinity for 1h
low salinity, 60h 1 mixed population whole organism mixed population at low salinity for 60 hours DV1 worms are kept at 1.5? salinity for 60h
standard conditions 1 mixed population whole organism mixed population grown under standard conditions DV1 worms are starved for 18-24h prior RNA isolation to prevent diatom contamination
starvation, 15h 1 mixed population whole organism mixed population starved for 15 hours DV1 worms are starved for 15h
starvation, 1h 1 mixed population whole organism mixed population starved for 1 hour DV1 worms are starved for 1h
starvation, 60h 1 mixed population whole organism mixed population starved for 60 hours DV1 worms are starved for 60h

SRP113706: Ageing in Macrostomum lignano

University Medical Center Groningen

Resilience to aging in the regeneration-capable flatworm Macrostomum lignano. (Mouton .. Berezikov, 2018)

Design: 16 conditions

Condition num. replicates Age Developmental stage Organism part Sex Strain Treatment
1 month, non-cut 6 1 month adult whole organism hermaphrodite DV1 non-cut
10 months, multiple-cut 3 10 months adult whole organism hermaphrodite DV1 multiple-cut
10 months, non-cut 3 10 months adult whole organism hermaphrodite DV1 non-cut
10 months, once-cut 3 10 months adult whole organism hermaphrodite DV1 once-cut
12 months, multiple-cut 3 12 months adult whole organism hermaphrodite DV1 multiple-cut
12 months, non-cut 3 12 months adult whole organism hermaphrodite DV1 non-cut
12 months, once-cut 3 12 months adult whole organism hermaphrodite DV1 once-cut
2 months, non-cut 6 2 months adult whole organism hermaphrodite DV1 non-cut
26 months, multiple-cut 3 26 months adult whole organism hermaphrodite DV1 multiple-cut
26 months, non-cut 3 26 months adult whole organism hermaphrodite DV1 non-cut
26 months, once-cut 3 26 months adult whole organism hermaphrodite DV1 once-cut
4 months, non-cut 3 4 months adult whole organism hermaphrodite DV1 non-cut
4 months, once-cut 3 4 months adult whole organism hermaphrodite DV1 once-cut
6 months, multiple-cut 3 6 months adult whole organism hermaphrodite DV1 multiple-cut
6 months, non-cut 3 6 months adult whole organism hermaphrodite DV1 non-cut
6 months, once-cut 3 6 months adult whole organism hermaphrodite DV1 once-cut

SRP114933: Macrostomum lignano strain:DV1 Raw sequence reads

University of Innsbruck

Organ specific gene expression in the regenerating tail of Macrostomum lignano. (Lengerer .. Ladurner, 2018)
Peter Ladurner Homepage

Design: 14 conditions

Condition num. replicates Breed Developmental stage Organism part Regeneration time
anterior, 2 days after removing the tail 2 DV1 regenerating adults anterior (reg. tail cut away) 2 days
anterior, 2 hours after removing the tail 2 DV1 regenerating adults anterior (reg. tail cut away) 2 hours
anterior, 3 days after removing the tail 2 DV1 regenerating adults anterior (reg. tail cut away) 3 days
anterior, 4 days after removing the tail 2 DV1 regenerating adults anterior (reg. tail cut away) 4 days
anterior, 4 hours after removing the tail 2 DV1 regenerating adults anterior (reg. tail cut away) 4 hours
anterior, 5 days after removing the tail 3 DV1 regenerating adults anterior (reg. tail cut away) 5 days
anterior, 7 days after removing the tail 3 DV1 regenerating adults anterior (reg. tail cut away) 7 days
whole organism, 2 days 2 DV1 regenerating adults whole organism 2 days
whole organism, 2 hours 2 DV1 regenerating adults whole organism 2 hours
whole organism, 3 days 2 DV1 regenerating adults whole organism 3 days
whole organism, 4 days 2 DV1 regenerating adults whole organism 4 days
whole organism, 4 hours 2 DV1 regenerating adults whole organism 4 hours
whole organism, 5 days 3 DV1 regenerating adults whole organism 5 days
whole organism, 7 days 3 DV1 regenerating adults whole organism 7 days

SRP174213: Sex allocation plasticity on a transcriptome scale: socially-sensitive gene expression in a simultaneous hermaphrodite

Bielefeld University

Design: 4 conditions

Condition num. replicates Group size Age Strain
isolated 4 isolated 66-69 days DV1
joined 4 joined 66-69 days DV1
octet 4 octet 66-69 days DV1
paired 4 paired 66-69 days DV1

Other

These studies are available in ENA, and the reads successfully align to our genomes.
We have decided not to include them in our analysis.
Either they failed to meet minimal criteria for inclusion, we've been asked to exclude them for data quality reasons, or we were unable to interpret the metadata.

SRP052579: Macrostomum lignano Positional Transcriptome

University of Basel

Macrostomum lignano genome initative website

4 runs in ENA

SRP053642: Macrostomum lignano Transcriptome or Gene expression

University College London

1 run in ENA

SRP059454: Macrostomum lignano small RNA and mRNA raw sequence reads

Cold Spring Harbor Laboratory

15 runs in ENA

SRP059553: Macrostomum lignano strain:DV1 | isolate:DV1 Genome sequencing and assembly

Cold Spring Harbor Laboratory

16 runs in ENA