title: GSM3019611: day2; Homo sapiens; RNA-Seq
library_construction_protocol: Viable cell suspensions of VPA treated hematopoietic stem cells at various time points were isolated and characterized using standard DAPI staining to determine viability. The bulk cellular suspensions were then characterized to determine cell density using a C-Chip DHC-N01 disposable hemocytometer.  A mixture of 5μl of 0.04% trypan blue (BioRad) and 5μl of the single cell suspension was loaded unto the hemocytometer and examined at 10X magnification, using the Invitrogen Evos FL Cell Imaging System-digital inverted microscope prior to loading on the 10X Genomics Chromium platform for cDNA generation.  The Chromium system was used as a microfluidic platform for 3' gene expression profiling of approximately 1528 to 4921 individual cells per Illumina HiSeq 2500 lane.  Prior to sequencing, the high diversity barcoding was conducted using standard manufacturer's protocol to separately index each cell's mRNA transcriptome using unique 3'-end tags using gel emulsion chemistry. Illumina paired-end sequencing libraries were then generated and sequenced from the fragments and the barcodes were leveraged to for differential expression analyses. Reverse-transcription was performed in the emulsion and cDNA was amplified before library construction (see Zheng et al., 2017 PMID: 28091601). Quality control and quantification of the amplified cDNA were assessed using the High-Sensitivity DNA Bioanalyzer kit. Library quality control and quantification were evaluated. GEM Drop-Seq, Chromium™ Single Cell 3' Library & Gel Bead Kit v1
attributes.tag: GEO Accession
attributes.value: GSM3019611