RNA-Seq of Schmidtea mediterranea: wnt1-RNAi 24h - SRA

SRX13928667: RNA-Seq of Schmidtea mediterranea: wnt1-RNAi 24h
1 ILLUMINA (Illumina HiSeq 4000) run: 48.3M spots, 7.3G bases, 2.5Gb downloads

Design: Wound samples (blastema and post-blastema) were obtained at 24h of regeneration after amputation on wnt1 RNAi animals. Three biological replicates were used per time point; each biological replicate was composed of eight animal fragments. At the corresponding time point animals were placed in a Petri dish with cold 1% HCl (diluted in water) for 2 and then transferred to a new Petri dish with cold PBS 1X. Two washes were performed with cold PBS 1X and animals were transferred to cold RNAlater for 20 placed in ice. Then, planarians were amputated in a Peltier Cell with a clean blade, to obtain the blastemas and post-blastemas. Fragments were washed with RNAlater (Invitrogen) and 50% RNAlater/Trizol; liquids were removed and 100ul of Trizol reagent (Invitrogen) was added, samples were then treated with DNase I (Roche). RNA-Seq libraries were prepared with KAPA Stranded mRNA-Seq Illumina Kit following the instructions provided by the manufacturer (Roche-Kapa Biosystems). Briefly, 500ng of total RNA was used for the poly-A fraction enrichment with oligo-dT magnetic beads, following the mRNA fragmentation. The strand specificity was achieved during the second strand synthesis performed in the presence of dUTP instead of dTTP. The blunt-ended double stranded cDNA was 3adenylated and Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq 4000 (Illumina) with a read length of 2x76bp using HiSeq 4000 SBS kit (Illumina) and HiSeq 4000 PE Cluster kit (Illumina), following the manufacturers protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturers software Real Time Analysis (RTA 2.7.7).

Submitted by: Universitat de Barcelona

Study: Wnt/beta-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration

PRJNA800775 • SRP356869 • All experiments • All runs

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For successful regeneration, the identity of the missing tissue must be specified according to the pre-existing tissue. Planarians are ideal for the study of the mechanisms underlying this process because the same field of cells can regrow a head or a tail according to the missing body part. After amputation, the differential activation of the WNT/betacatenin signal specifies anterior versus posterior identity. Initially, both wnt1 and notum (Wnt inhibitor) are expressed in all wounds, but 48 hours later they are restricted to posterior or anterior facing wounds, respectively, by an unknown mechanism. Here we show that 12 hours after amputation the chromatin accessibility of cells in the wound region changes according to the polarity of the pre-existing tissue in a WNT/betacatenin-dependent manner. Genomic analyses suggest that homeobox transcription factors and chromatin-remodeling proteins are direct WNT/\betacat targets, which trigger the expression of posterior effectors. Finally, we identified FoxG as a wnt1 up-stream regulator, probably via binding to its first intron enhancer.

Sample: Wnt/Bcat signalling chromatin remodeling planarian regeneration: RNAseq wnt1-RNAi 24h

SAMN25282218 • SRS11775773 • All experiments • All runs

Organism: Schmidtea mediterranea

Library:

Name: WNTBCAT_repNAseq_WNT1_24h_rep3

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Runs: 1 run, 48.3M spots, 7.3G bases, 2.5Gb

Run	# of Spots	# of Bases	Size	Published
SRR17766286	48,291,339	7.3G	2.5Gb	2022-12-18

ID:: 19418211

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