Dataset View [GSE57872]

TitleSingle cell RNA-seq of primary human glioblastomas
ArticleBernstein BE,Regev A,Suvà ML,Rozenblatt-Rosen O,Louis DN,Martuza RL,Curry WT,Nahed BV,Cahill DP,Wakimoto H,Gillespie SM,Shalek AK,Trombetta JJ,Tirosh I,Patel AP.Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.Science (New York, N.Y.).2014 Jun 20
Bio ProjectBioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA248302
SraSRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP042161
Overall DesginOperative specimens from five glioblastoma patients (MGH26, MGH28, MGH29, MGH30, MGH31) were acutely dissociated, depleted for CD45+ inflammatory cells and then sorted as single cells (576 samples). Population controls for each tumor were isolated by sorting 2000-10000 cells and processed in parallel (5 population control samples). Single cells from two established cell lines, GBM6 and GBM8, were also sorted as single cells (192 samples).
SummaryWe report transcriptomes from 430 single glioblastoma cells isolated from 5 individual tumors and 102 single cells from gliomasphere cells lines generated using SMART-seq. In addition, we report population RNA-seq from the five tumors as well as RNA-seq from cell lines derived from 3 tumors (MGH26, MGH28, MGH31) cultured under serum free (GSC) and differentiated (DGC) conditions. This dataset highlights intratumoral heterogeneity with regards to the expression of de novo derived transcriptional modules and established subtype classifiers.
Experimental ProtocolSingle cells were sorted into TCL buffer (Qiagen, 1031576) + 1% beta-mercaptoethanol and RNA-seq libraries generated using SMART-seq (modified from Shalek, et. al, Nature 2013) .; Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096) used for barcoding according to manufacturer's protocol
Data processingBasecalls performed using Bcl2fastq 1.8 (Illumina); Paired-end 25bp reads were mapped to the UCSC human transcriptome (hg19) by Bowtie (version 1.4.1, with parameters -n 0 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 –S); Expression levels of all genes were estimated by RSEM (version 1.2.3, using the option estimate-rspd and default parameters) using only reads with exact matches; TPM values as defined by RSEM were added a value of 1 (to avoid zeros) and then log2-transformed. 5,948 genes with the highest composite expression either across all cells combined (average log2(TPM)>4.5) or within a single tumor (average log2(TPM)>6 in at least one tumor) were included. Cells expressing less than 2,000 of these 5,948 genes were excluded. Data was centered by subtracting the mean.; Genome_build: hg19; Supplementary_files_format_and_content: Tab delimited file containing normalized, centered transcripts per million (TPM) values for 5,948 genes in each single cell and population controls
Public OnPublic on Jun 12 2014

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