GSM4455442: LB2-2: More affected - replicate during late-treatment run; Homo sapiens; RNA-Seq
Skin biopsies were flash frozen on dry ice and stored at -80°C. Qiazol (QIAGEN N.V., Venlo, Netherlands) solution was added to frozen samples, and RNA extraction was performed using a Fastprep 24 bead-beating homogenizer (MPBio, Santa Ana, CA; Lysing Matrix D) and the RNeasy Minikit (QIAGEN). Stranded paired-end libraries were generated from 1µg total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, Inc.) and sequenced on an Illumina HiSeq4000 (2 x 76bp read length). Adapters were IDT for Illumina - TruSeq RNA UD Indexes to eliminate index misassignment. Amplification was performed using 10 cycles which was optimized for the input amount and to minimize over-amplification. Libraries were pooled in equimolar amounts for sequencing. Sequencing was performed in two batches according to when the skin biopsies were collected. In the first batch, a more affected and a less affected site were biopsied and 2 technical replicates of each were sequenced at an average of 45 million reads per technical replicate. For the second batch, a late-treatment biopsy was collected and sequenced together with a third replicate of the original two biopsy samples at an average read depth of 235 million reads.
GEO Accession
GSM4455442