title: GSM4873588: TZPL08_Placenta of control 6-somite embryo  (Jx1 cross) #4; Mus musculus; RNA-Seq
library_construction_protocol: Total RNA was isolated from placentas by acid-phenol extraction using RNA-Bee (Tel-TEST) followed by isopropanol precipitation. Genomic DNA was removed with the DNA-free Kit (Ambion). Total RNA ibraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems, Wilmington, MA USA) following kit parameters. In short, RNA was sheared for 6 min at 86 oC to produce 300-400 bp fragments and it was converted to cDNA. After repairing the ends the cDNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA) and amplified using 11 cycles of PCR. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).  Individually indexed libraries were pooled, and paired end 75 bp sequencing was performed on an Illumina NextSeq 500 sequencer using a 150 bp HO sequencing kit (v2) (Illumina Inc., San Diego, CA, USA), with all libraries run across 5 flowcells to return a minimum read depth of 40M read pairs per library. Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0. Allele-specific, stranded, paired-end total RNA seq
attributes.tag: GEO Accession
attributes.value: GSM4873588