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| Status |
Public on Jan 17, 2017 |
| Title |
ATACseq_replicate2 |
| Sample type |
SRA |
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| Source name |
Sperm
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| Organism |
Mus musculus |
| Characteristics |
strain background: CD1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ATAC-seq, the purified sperm pellet was resuspended in the transposase reaction mix and incubated for 30 min at 37°C. Following incubation, sperm were lysed, incubated with Proteinase K at 55°C for 2 hr, and gDNA was isolated by phenol:chloroform:isoamyl alcohol and EtOH precipitation. Library amplification was done with 2x KAPA HiFi mix and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 sec; and 10-11 cycles at 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
ATAC-seq
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| Data processing |
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm9 using Bowtie 0.12.7 for ATAC-seq. ATAC-seq reads were aligned using default parameters except -X 2000 -m 1. Duplicates were removed using Samtools. To adjust for fragment size, we aligned all reads as + strands offset by +4 bp and – strands offset by -5 bp (Buenrostro et al. 2013). To separate nucleosome-free (THSS) and mono-nucleosome (Nucleosome) fragments, we chose reads 50-115 bp 180-247 bp in length, respectively. Mono-nucleosome reads were analyzed using DANPOS2 (Chen et al. 2013). MACS2 was used for peak calling with nucleosome-free reads (Liu 2014). For generating wiggle files, we combined each replicates.
Genome_build: mm9
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| Submission date |
Mar 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoonhee Jung |
| E-mail(s) |
yoonhee.jung@emory.edu
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| Phone |
4047274250
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| Organization name |
Emory university
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| Department |
Human Genetics
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| Lab |
Corces lab
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| Street address |
615 Michael Street
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| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE79225 |
Mammalian sperm exhibit epigenetic priming of embryonic and adult regulatory landscapes (ATAC-Seq) |
| GSE79230 |
Mammalian sperm exhibit epigenetic priming of embryonic and adult regulatory landscapes |
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| Relations |
| BioSample |
SAMN04557224 |
| SRA |
SRX1631867 |
| 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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