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Sample GSM2723773 Query DataSets for GSM2723773
Status Public on Aug 01, 2017
Title WT_P10_1_ATAC
Sample type SRA
 
Source name retina
Organism Mus musculus
Characteristics strain: C57BL/6
developmental stage: postnatal day 10
tissue: retina
Extracted molecule genomic DNA
Extraction protocol ATAC-seq library preparation was performed as described (Buenrostro et al., 2013) with minor modifications. Briefly, for each experiment, 2 × 105 - 5 × 105 dissociated retinal cells were washed twice with PBS (Lonza, 17-516F) containing Proteinase Inhibitor Cocktail (Sigma-Aldrich P8340), incubated with 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.3% IGEPAL CA-630) on ice for 10 min and centrifuged at 500 g for 10 min at 4°C. After centrifugation, the pellet was immediately incubated with 50 μL of Tn5 transposition reaction mix (25 μL TD buffer, 2.5 μL TDE1 (Nextera DNA Library Prep Kit, Illumina, FC-121-1030) and 22.5 μL nuclease-free water) at 37°C for 30 min. After purification with QIAGEN MinElute PCR Purification Kit (QIAGEN, 28006), transposed DNA fragments were amplified with NEBNext High-Fidelity 2 × PCR Master Mix (New England Biolabs, M0541) for 5 cycles using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. 5 μL of each library was amplified in a 25 μL qPCR reaction with KAPA SYBRFAST qPCR Kit (Kapa Biosystems, KK4603) to estimate the optimum number of additional cycles to finish amplification of the remaining 45 μL library.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description processed data file:
ATAC-Dev-Ret_M_N-P10.free.bw
Data processing Basecalls performed using CASAVA
After trimming nextra adapter with cutadapt(v 1.13), we used BWA (version 0.5.9-r26-dev, default parameter) to align the reads to mouse genome mm9(MGSCv37 from Sanger), Picard(version 1.65(1160)) then have been used for marking duplicated reads. Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1804” version 0.1.18 (r982:295)).
center 80bp of nucleosome free reads were used generate bigwig file to view on IGV (version 2.3.40).
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig
 
Submission date Jul 31, 2017
Last update date May 15, 2019
Contact name Beisi Xu
E-mail(s) beisi.xu@stjude.org
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL21103
Series (2)
GSE87064 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
GSE102092 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [ATAC-Seq_Mm]
Relations
BioSample SAMN07428763
SRA SRX3050831

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

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