characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2015-09-17T17:02:06Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T18:43:25Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2733018
characteristics.characteristic: External Id
characteristics.text: College of Veterinary Medicine, Shaanxi Center for Stem Cell Engineering and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
characteristics.characteristic: INSDC center name
characteristics.text: 2015-09-17T17:02:06Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T18:43:25Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS494777
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2634:iPS-g
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: stem cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000034
characteristics.characteristic: cell type
characteristics.text: pig
characteristics.characteristic: common name
characteristics.text: The piPSC-g lines derived in our labwith culture media added both bFGF and LIF also showed the flattened morphology Protocols: The RNA library construction and deep sequencing were performed in CapitalBio Corporation (Beijing, China), using the TruSeq Small RNA Sample Preparation Kit and sequencing Kit (Illumina, CA) according to the manufacturer’s protocol. Briefly, 4mg of total RNA was ligated with the 39and 59 adapters successively. After reverse transcription, a 12 cycles of PCR reaction was performed. The resultant library was then qualified by the Agilent 2100 High Sensitivity DNA chip and quantified by Qubit and qPCR. The cluster generation and sequencing were performed on the cBot and Hiseq2000 respectively, following the manufacturer’s standard cBot and sequencing protocols. The adapter sequences were removed from both ends of Solexa reads. A per script was developed to remove the low quality reads, empty tags (adaptor sequence only) and tags less than 18 nt or more than 31 nt. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index odes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H-). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated. Total RNA was isolated from cell cultures or snap-frozen tissues, in biological triplicates or greater, using TRIzol extraction and purified with the Qiagen RNA Purification Kit.
characteristics.characteristic: description
characteristics.text: Sus scrofa
characteristics.characteristic: organism
characteristics.text: Sus scrofa
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9823
characteristics.characteristic: organism
characteristics.text: Sus scrofa
characteristics.characteristic: scientific_name
characteristics.text: iPS-g
characteristics.characteristic: title