title: GSM4013112: Single cell fibroblast TS1B_C55; Homo sapiens; OTHER
library_construction_protocol: Single-cell capture was performed using the C1 single-cell auto prep system (Fluidigm) following the manufacturer's procedure. The integrated fluidic circuit used for the study is the C1™ Single-Cell mRNA Seq IFC, 17–25 μm with a capacity of 96 chambers. During the capture, all 96 chambers were inspected under an inverted phase contrast microscope; only chambers containing a non-damaged single cell were considered for downstream analysis. SMARTer Ultra Low RNA kit for Illumina sequencing (version 2, Clontech) was used for the cell lysis and cDNA synthesis. Libraries were prepared with 0.3 ng of pre-amplified cDNA using Nextera XT DNA kit (Illumina) Libraries were sequenced on an Illumina HiSeq2000 sequencer as 100 bp single ended reads. RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 10 million reads and/or cells with <10% of expressed genes (total number of 56680 genes) were excluded from the analyses.