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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 01, 2016 |
| Title |
T1-FAIRE |
| Sample type |
SRA |
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| Source name |
astrocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
genotype: truncated SV40 T-antigen
passages: 12-15
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| Growth protocol |
DMEM+10% FBS, 5% CO2
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| 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).
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| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Sep 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Miller |
| E-mail(s) |
rmiller@med.unc.edu
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| Organization name |
University of North Carolina - Chapel Hill
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| Street address |
6109B Neuroscience Research Building
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| City |
Chapel Hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN04100016 |
| SRA |
SRX1270155 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1889815_T2-FAIRE.bw |
1.1 Gb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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