GSM3109132: 1576; Homo sapiens; RNA-Seq
Library preparation and sequencing. RNA was extracted using Qiagen miRNeasy Mini Prep Kit (catalog # 74106). Quality of RNA was assessed on the Agilent 2100 Bioanalyzer. Samples with RIN greater than or equal to 8 were sent to the Next-Generation Sequencing Core at the Perelman School of Medicine at the University of Pennsylvania. Libraries were made using Illumina TruSeq Stranded Total RNA Library Prep Kit (catalog # 20020597) and sequenced using 125bp paired-end on HiSeq 2500 Platform. We used ATAC-seq to assess chromatin accessibility with slight modifications to the published protocol {Buenrostro:2015be}. Approximately 5e4 fresh cells were collected at 500 g, washed in PBS, and nuclei extracted with cold lysis buffer. Pellets were subjected to transposition containing Tn5 transposases (Illumina) at 37 °C for 30 min, followed by purification using the DNA Clean-up and Concentration kit (Zymo). Libraries were PCR amplified using Nextera barcodes, with the total # of cycles empirically determined using SYBR qPCR. Amplified libraries were purified and quantified using bioanalyzer, nanodrop and qPCR (KAPA) analysis. Libraries were multiplexed and 2x75 bp sequencing was performed using an Illumina NextSeq 500.
GEO Accession
GSM3109132