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Sample GSM2124786 Query DataSets for GSM2124786
Status Public on Jun 19, 2016
Title GBM Sample 2 (sample 2)
Sample type SRA
 
Source name GBM
Organism Homo sapiens
Characteristics cell type: CD11b+ human glioblastoma-associated microglia/monocytes
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). Total RNA was converted into libraries of double stranded cDNA molecules as a template for high throughput sequencing following the manufacturer’s recommendations using the Illumina TruSeq RNA Sample Preparation Kit v2
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description GBM Sample 2
Data processing Base calling and de-multipexing was performed using CASAVA version 1.8
RNAseq reads were aligned to UCSC hg19 using TopHat2 (v 2.0.12), allowing for 2 mismatches.
For each sample, a count table for all genes was generated using R function summarizeOverlaps from the R/Bioconductor package GenomicAlignments (v 1.7.3) using only the primary alignments of each read.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
 
Submission date Apr 15, 2016
Last update date May 15, 2019
Contact name Sonali Arora
E-mail(s) sarora@fredhutch.org
Organization name FHCRC
Street address 1100 Fairview Ave N,
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL18460
Series (1)
GSE80338 Human glioblastoma-associated microglia/monocytes express a distinct RNA profile compared to human control and murine samples
Relations
BioSample SAMN04549848
SRA SRX1631223

Supplementary file Size Download File type/resource
GSM2124786_fpkm_Sample2.txt.gz 248.4 Kb (ftp)(http) TXT
GSM2124786_raw_Sample2.txt.gz 122.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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