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Sample GSM1395934 Query DataSets for GSM1395934
Status Public on Jun 12, 2014
Title Single cell mRNA-seq_MGH31_E08
Sample type SRA
 
Source name Single cell mRNA-seq_MGH31
Organism Homo sapiens
Characteristics patient id: MGH31
cell type: Glioblastoma
subtype: Mes
Treatment protocol Differentiated glioma cells were generated by transitioning gliomasphere cultured cells to DMEM + 10% FCS for 7 days.
Growth protocol Gliomasphere cell lines were cultured in Neurobasal Medium supplemented with 1x B27, 0.5x N2, and 10 ng/ml EGF/FGF.
Extracted molecule total RNA
Extraction protocol Single 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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description processed data file: GBM_data_matrix.txt
Data processing Basecalls 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
 
Submission date May 21, 2014
Last update date May 15, 2019
Contact name Anoop Patel
Organization name Massachusetts General Hospital
Department Pathology
Lab Brad Bernstein
Street address 185 Cambridge St
City BOSTON
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL16791
Series (1)
GSE57872 Single cell RNA-seq of primary human glioblastomas
Relations
BioSample SAMN02797069
SRA SRX549641

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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