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Sample GSM1889814 Query DataSets for GSM1889814
Status Public on Feb 01, 2016
Title T2-FAIRE
Sample type SRA
 
Source name astrocytes
Organism Mus musculus
Characteristics strain: C57BL6
genotype: truncated SV40 T-antigen
passages: 12-15
Growth protocol DMEM+10% FBS, 5% CO2
Extracted molecule genomic DNA
Extraction protocol FAIRE was performed as described previously (Simon 2012).
TruSeq libraries were constructed as per manufacturer's recommendations (NEB cat # E7370).
 
Library strategy FAIRE-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with quality score greater than 20 for 90% of bases were retained, and aligned to the reference mouse genome (mm9) with GSNAP (Wu and Nacu 2010) using a k-mer size of 15, indel penalty of 5, and allowing 1 mismatch. Reads aligning to more than four locations or overlapped blacklisted regions of the mouse genome were removed.
Peaks were identified for each sample using Fseq (Boyle et al. 2008).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of raw FAIRE-seq signal
 
Submission date Sep 21, 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)
GSE73262 Core pathway mutations induce de-differentiation of murine astrocytes into glioblastoma stem cells that are sensitive to radiation, but resistant to temozolomide (FAIRE-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 SAMN04100015
SRA SRX1270154

Supplementary file Size Download File type/resource
GSM1889814_T1-FAIRE.bw 915.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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