characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2015-11-13T17:10:00Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T19:57:01Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2676302
characteristics.characteristic: External Id
characteristics.text: Genomnia srl
characteristics.characteristic: INSDC center name
characteristics.text: 2015-11-13T17:10:00Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T19:57:01Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS516327
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2811:MCFS
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: MCF7
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001203
characteristics.characteristic: cell line
characteristics.text: highly tumorigenic breast cancer mammospheres (MCFS)
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: The MCF7 breast cancer cell line MCF7 was purchased from the American Type Culture Collection (ATCC; Manassas, VA). MCFS cells were derived in our laboratory from the MCF7 cell line (Ponti et al. 2005) and propagated as floating mammospheres. Cell vitality was assessed by Trypan Blue exclusion assay (at least 95%) before starting any experiment. Authentication of cell lines by STR DNA profiling analysis was performed at the A.O. Niguarda Ca Granda Hospital in Milan. Total RNA from 5000 MCF-7 and MCF-S cells was extracted following Agencourt RNAdvance Cell v2 (Beckman Coulter, MA, USA) protocol using Agencourts patented SPRI paramagnetic bead. Manufacturer instructions were followed with the following exception regarding DNAse treatment step: Ambion TURBO DNA-free (Life Technologies technologiesCorporation, Carlsbad, CA, USA) was used instead of the one suggested in the kit. Ninety ng of total RNA was amplified, prior to transcriptome sequencing, using Ribo-SPIA technology developed by NuGEN following Ovation RNA-seq (2009, NuGEN Technologies, Inc.) manufacturers instructions. The amplified cDNA was purified prior to subsequent processing for library construction using RNA Clean purification magnetic beads (Beckman Coulter Genomics, MA, USA) as suggested in the protocol. Double stranded DNA was quantified with Qubit ds DNA BR Assay Kits (Invitrogen, Ltd., UKLife technologies) and its size distribution was checked using the Agilent RNA Nano kit (Agilent Technologies, Inc.) following the manufacturers instructions. DNA library, one for each sample, was constructed following the SOLiD 3 Plus System Library Preparation Guide (Life Technologies Corporation, Carlsbad, CA, USA) manufacturers instructions. Four emulsions PCR, two for each library, were manually performed following Applied Biosystems SOLiD 3 Plus System Templated Bead Preparation Guide, according to the manufacturers instructions (Life Technologies Corporation, Carlsbad, CA, USA). The libraries and emulsions quality were checked in a workflow analysis (WFA) run following SOLiD 3 Plus System Instrument Operation Guide (Life Technologies Corporation, Carlsbad, CA, USA).
characteristics.characteristic: description
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: frozen specimen
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000922
characteristics.characteristic: specimen with known storage state
characteristics.text: MCFS
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001203
characteristics.characteristic: title