NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1959749 Query DataSets for GSM1959749
Status Public on Feb 01, 2016
Title TRP2-RNA
Sample type SRA
 
Source name astrocytes
Organism Mus musculus
Characteristics strain: C57BL6
genotype: truncated SV40 T-antigen, KRas(G12D), Pten del/del
passages: 12-15
Treatment protocol Total RNA was extracted from cell pellets (Qiagen RNAeasy kit, Germantown, MD), followed by library preparation using a Stranded mRNA-seq kit (KAPA Biosystems, Wilmington, MA) according to the manufacturer's instructions.
Growth protocol DMEM+10% FBS, 5% CO2
Extracted molecule polyA RNA
Extraction protocol Library sequencing was performed on a NextSeq500 system with a 75 cycle High Output kit (Illumina, San Digo, CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Reads were truncated to 50bp then filtered using TagDust and only reads with quality score greater than 20 for 90% of bases were retained. Reads were then aligned to the reference mouse genome (mm9) with GSNAP using a k-mer size of 15, indel penalty of 5, and allowing 1 mismatch. Reads aligning to blacklisted regions of the mouse genome were removed.
Transcript abundance was estimated by computing raw counts or RPKM using RefSeq gene models aggregated by gene symbol.
Genome_build: mm9
Supplementary_files_format_and_content: Expression matrix
 
Submission date Dec 01, 2015
Last update date May 15, 2019
Contact name Ryan Miller
E-mail(s) rmiller@med.unc.edu
Organization name University of North Carolina - Chapel Hill
Street address 6109B Neuroscience Research Building
City Chapel Hill
State/province North Carolina
ZIP/Postal code 27599
Country USA
 
Platform ID GPL19057
Series (2)
GSE75589 Core pathway mutations induce de-differentiation of murine astrocytes into glioblastoma stem cells that are sensitive to radiation, but resistant to temozolomide (RNA-seq)
GSE75592 Core pathway mutations induce de-differentiation of murine astrocytes into glioblastoma stem cells that are sensitive to radiation, but resistant to temozolomide
Relations
BioSample SAMN04305440
SRA SRX1457966

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap