title: E-MTAB-607:Smed_Illumina_1
organism: Schmidtea mediterranea
attributes.tag: Alias
attributes.value: E-MTAB-607:Smed_Illumina_1
attributes.tag: Batch
attributes.value: 1
attributes.tag: Broker name
attributes.value: ArrayExpress
attributes.tag: Description
attributes.value: Protocols: 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. 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. 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).
attributes.tag: Genotype
attributes.value: wild_type
attributes.tag: INSDC center name
attributes.value: DKFZ-GPCF
attributes.tag: INSDC first public
attributes.value: 2011-07-14T11:52:50Z
attributes.tag: INSDC last update
attributes.value: 2013-11-04T20:04:51Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: OrganismPart
attributes.value: pre-pharyngeal fragment, regenerating the head
attributes.tag: SRA accession
attributes.value: ERS026150
attributes.tag: Sample Name
attributes.value: ERS026150
attributes.tag: Sex
attributes.value: asexual
attributes.tag: StrainOrLine
attributes.value: BCN-10
attributes.tag: Title
attributes.value: Smed_Illumina_1