{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Thomas Sandmann"],"study_type":["RNA-seq of coding RNA"],"organism":["Schmidtea mediterranea"],"species":["Schmidtea mediterranea"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-607"],"description":["The head-regeneration transcriptome of the planarian Schmidtea mediterranea"],"repository":["biostudies-arrayexpress"],"pubmed_title":["The head-regeneration transcriptome of the planarian Schmidtea mediterranea"],"sample_protocol":["Growth Protocol - Animals were kept at 20C in Montjuic solution (1 mM CaCl2, 0.1 mM KCl, 1.6 mM NaCl, 1.2 mM NaHCO3, 0.1 mM MgCl2, 1mM MgSO in water) and fed with veal liver once per week.","Nucleic Acid Extraction - Total RNA was extracted from planarian fragments using Trizol. 0.5 microgram of polyA RNA was isolated from total RNA using the MicroPoly(A)Purist kit (Ambion), fragmented and precipitated. First strand cDNA was synthesized using SuperScript II (Invitrogen) and the second strand was added using RNAseH and DNA Polymerase I. cDNA was purified with the QIAquick PCR purification kit (QIAGEN) and ends were repaired with Klenow DNA polymerase. The 3 prime ends were adynlated with Klenow exo (3 prime to 5 prime exo minus) enzyme and ligated to the sequencing adapters. cDNA templates were separated by Agarose gel electrophoresis and ca. 200 bp sequences were selected. Templates for sequencing were PCR amplified using Phusion DNA polymerase (Finnzymes Oy) and purified with the QIAquick PCR purification kit (QIAGEN).","Sample Processing - For each sample, 5 planarian trunks were dissected from heads and tails. For control samples, samples were frozen immediately after dissection. The 1 and 6 hr samples were generated the following way:  At timepoint 0, the head and the tail was amputated, so there were now 3 pieces: one animal => head + trunk + tail. These 3 pieces were kept in the same culture vessel together and all allowed to regenerate. Each piece started to regenerate at each wound.  After 1 hr or 6 hrs, all three pieces (including whatever regenerated in this short period of time) were extracted together (head + trunk + tail). .","Nucleic Acid Extraction - Total RNA was extracted using TRIzol (Invitrogen). Strand-specific sequencing libraries were prepared from polyA RNA selected material using Applied Biosystems Whole Transcriptome Library Preparation protocol (Part number 4409491 Rev. C). In brief, 1 mg of polyA RNA was isolated using the MicroPoly(A)Purist kit (Ambion), fragmented using RNAse III (Applied Biosystems) and column purified. SOLiD sequencing adapters were ligated to the RNA RNA using components from the SOLiD Small RNA Expression Kit (Applied Biosystems). Afterwards, the RNA was reverse transcribed using ArrayScript Reverse Transcriptase and cDNA purified using the MinElute PCR purification kit (Qiagen). cDNA fragments were separated using by electropheresis on Novex 6% TBE-Urea gels, stained with SYBR Gold nucleic acid gel stain and sequences between 100-200 nt were selected. Afterwards, fragments were PCR amplified using AmpliTaq for 15 cycles to obtain templates for emulsion PCR and sequencing.","Sample Processing - Asexual planarians of the species Schmidtea mediterranea were starved for one week prior to decapitation with a razor blade. Regeneration was allowed to occur for 16 different periods of time (30 min, 1, 2, 3, 4, 5, 6, 8, 10, 12, 16, 18, 24, 36, 48, 72h). A second cut anterior to the pharynx (pre-pharyngeal cut) was performed to separate the anterior regenerating part from the rest of the body. 8 planarian pre-pharyngeal pieces from similar time points were pooled (Library 1: 30 min and 1h, four animals each; Library 2: 2h and 3h, four animals each; Library 3: 4, 5, 6, and 8h, two animals each; Library 4: 10, 12, 16, and 18h, 2 animals each; Library 5: 24, 36, 48, and 72h, 2 animals each), and immediately deep-frozen. 16 non-regenerating pieces served as two independent biological replicates (8 animals each; Library 6 and 7). Samples were processed in two batches: material from control Library 6 was processed together with Libraries 1-3, while contrl Library 7 was processed together with Libraries 4 and 5."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Thomas Sandmann","Thomas Sandmann, Matthias C. Vogg, Suthira Owlarn, Michael Boutros, and Kerstin Bartscherer"],"additional_accession":[]},"is_claimable":false,"name":"The head-regeneration transcriptome of the planarian Schmidtea mediterranea","description":"The head-regeneration transcriptome of the planarian Schmidtea mediterranea","dates":{"release":"2011-07-15T00:00:00Z","modification":"2022-02-03T10:34:07.963Z","creation":"2022-02-03T10:34:07.963Z"},"accession":"E-MTAB-607","cross_references":{"ENA":["ERP000581"],"EFO":["EFO_0003738"]}}