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| Status |
Public on Oct 11, 2019 |
| Title |
Macaque replicate 3 |
| Sample type |
SRA |
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| Source name |
Skin fibroblast cells
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| Organism |
Macaca mulatta |
| Characteristics |
coriell id: AG08308
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| Growth protocol |
Growth media consisted of Gibco's MEM (10370-021), L-Glutamine (25030-081), Pen/Strep (15140-122), and 10% FBS (Hyclone SH30070).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were grown in culture then pelleted before immediately proceeding to DNase-seq library preparations. All DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106). Briefly, cells were lysed and incubated at 37¡C for various times (5 min to 1 hour) and optimal DNase digestion was confirmed by pulsed field gel electrophoresis (Song L and Crawford GE. Cold Spring Harbor protocols 2010(2):pdb prot5384).
DNase-seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106).
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
Due to the use of MmeI to generate DNase-seq libraries, sequencing reads were trimmed to 20 bases using a custom perl script.
Reads for each species were mapped to its native genome using Bowtie version 0.12.9 (parameters: -trim5 0 --trim3 0 -m 1 -l 20) as part of a custom two-step pipeline. In the first step (“tier 1”), reads were required to match to a unique location with no mismatches (parameter: -n 0). In the second step (“tier 2”), unmapped reads from step one were re-mapped with a relaxed mismatch parameter of one mismatch (parameter: -n 1). Reads that mapped to multiple locations or had more than one mismatch were discarded.
Samtools version 0.1.19-44428cd was used to convert the sam files from each step to bam files, merge them into one file, and remove duplicate reads (defined as having the same chromosomal position).
Bedtools v2.17.0 was used to convert the bam files to bed files.
Reads from the non-human samples were converted from their native genome coordinates to the human hg19 genome coordinates using a three-step process that removed reads that did not have a one-to-one relationship between the genomes. In each step, read coordinates were converted from one genome to the other using the UCSC liftOver software with a minMatch parameter of 0.8, which requires that 80% of the read maps to the new genome. Note that this parameter filters only on genomic coverage, not sequence identity. In the first step, read coordinates were converted from their native genome to hg19. Read coordinates that successfully lifted to hg19 were then lifted back to the native genome. Read coordinates that did not lift back to the same coordinates on the native genome were removed. Reads that did lift back to the same coordinates were lifted back to hg19. An additional filtering step was added to ensure the reads did not map to a duplicated region. In that step, overlapping reads were merged into a region, and that region was lifted from the native genome to hg19. Regions that failed to lift uniquely to hg19 were flagged and reads that overlapped them were removed.
Because some of the samples were from males and some were from females, we removed reads that mapped or lifted over to the human X or Y chromosomes to eliminate any sex-specific bias.
Genome_build: hg19 for human, panTro4 for chimpanzee, gorGor3 for gorilla, ponAbe2 for orangutan, rheMac3 for macaque
Supplementary_files_format_and_content: bed files contain hg19 coordinates for the reads
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| Submission date |
Mar 29, 2019 |
| Last update date |
Oct 11, 2019 |
| Contact name |
Gregory Crawford |
| E-mail(s) |
greg.crawford@duke.edu
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| Organization name |
Duke University
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| Street address |
101 Science Drive
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platform ID |
GPL9160 |
| Series (1) |
| GSE129034 |
Comparison of chromatin accessibility between human and non-human primates |
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| Relations |
| BioSample |
SAMN11285970 |
| SRA |
SRX5600572 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3692007_macaque3.full_read_set.bed.gz |
165.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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