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| Status |
Public on Aug 01, 2017 |
| Title |
WT_P21_1_ATAC |
| Sample type |
SRA |
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| Source name |
retina
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: postnatal day 21
tissue: retina
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| 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
processed data file:
ATAC-Dev-Ret_M_N-P21.free.bw
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| 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
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| Submission date |
Jul 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
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| Organization name |
St Jude Children's Research Hosipital
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| Department |
Center for Applied Bioinformatics
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| 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] |
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| Relations |
| BioSample |
SAMN07428760 |
| SRA |
SRX3050834 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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