title: GSM3755952: H2C KD lung met sh4 mouse 10 met 1; Mus musculus; OTHER
library_construction_protocol: Metastases were dissociated using a sterile disposable pestle in a microcentrifuge tube in tail lysis buffer (100 mM Tris pH8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl). 160 ug of Proteinase K (Invitrogen) was added to the tube and contents were incubated at 55 ℃ overnight then for an additional 1hr with shaking at 1400 rpm. Genomic DNA was then isolated from the dissociated metastases using the DNA miniprep kit (Zymo Research) according to the manufacturer's instructions. DNA quality was tested using the Agilent 2200 TapeStation electrophoresis system, and samples were sent for sequencing For mRNA samples: mRNA sequencing was performed using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry. Sample reads were trimmed to remove adapters and low-quality bases using Trimmomatic software and aligned with the reference mouse mm9 genome and Ensemble v70 transcripts using Tophat software. RNA mapping statistics were calculated using Picard software. Library complexity was measured by unique fragments in the mapped reads using Picard's MarkDuplicate utility.
attributes.tag: GEO Accession
attributes.value: GSM3755952