 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 30, 2019 |
| Title |
11_46 ATAC-Seq |
| Sample type |
SRA |
| |
|
| Source name |
CA1
|
| Organism |
Macaca mulatta |
| Characteristics |
macaque id: Rhesus 11
tissue: brain
gender: female
age(years): 9.8
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A total amount of 10,000 cells at 500g for 5 min, cells were lysed using cold lysis buffer. Nuclei were spun at 500g for 10 min using a refrigerated centrifuge. The pellet was resuspended in the transposase reaction mix for 30 min at 37 °C, sample was purified using a Qiagen MinElute kit.
The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL. Libraries were amplified for a total of 10–15 cycles. Libraries were sequenced on Illumina NextSeq 500 (Next500 kit v2 High Output 150 cycles).
ATAC-seq:A total amount of 10,000 cells at 500g for 5 min, cells were lysed using cold lysis buffer. Nuclei were spun at 500g for 10 min using a refrigerated centrifuge. The pellet was resuspended in the transposase reaction mix for 30 min at 37 °C, sample was purified using a Qiagen MinElute kit.
ATAC-seq: The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL. Libraries were amplified for a total of 10–15 cycles. Libraries were sequenced on Illumina NextSeq 500 (Next500 kit v2 High Output 150 cycles).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ATAC-seq: paired-end reads were aligned to the rhesus macaque genome (Mmul 8.0.1, downloaded from ENSEMBL), using bwa mem (v0.7.12) with -M parameter. First, PCR duplicates were removed using Picard (v1.119). Reads mapped to mitochondrial DNA were then excluded. Only uniquely mapped and properly paired reads with insert size less than 2kb and mapping quality over 30 were kept for downstream analysis. ATAC-seq peak calling was performed with Genrich (v0.6, available at https://github.com/jsh58/Genrich, parameters: -r -m 30 -q 0.05 -a 200 -j -y -e MT,Y -b) for each region. The BED files recording ATAC-seq signals were converted to BedGraph using “bedtools genomecov” and scaled by a factor of 1,000,000/LibrarySize. Then the scaled BedGraph files were converted to BigWig files using bedGraphToBigWig for genome visualization.
Genome_build: Mmul 8.0.1
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Dec 26, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
keying Lu |
| E-mail(s) |
[email protected]
|
| Organization name |
Sichuan university
|
| Department |
State Key Laboratory of Biotherapy
|
| Street address |
Wuhou
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610000 |
| Country |
China |
| |
|
| Platform ID |
GPL21120 |
| Series (1) |
| GSE128537 |
Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain |
|
| Relations |
| BioSample |
SAMN13683264 |
| SRA |
SRX7442944 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4233081_11_46.bw |
1.1 Gb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
