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Sample GSM3679594 Query DataSets for GSM3679594
Status Public on Dec 30, 2019
Title 3_32 ATAC-seq
Sample type SRA
Source name posterior cingular gyrus
Organism Macaca mulatta
Characteristics macaque id: Rhesus 3
tissue: brain
gender: male
age: 10 years
Extracted molecule genomic DNA
Extraction protocol RNA-seq:RNA degradation and contamination was detected by 1% agarose gels; Then, RNA purity was checked using the kaiao K5500® Spectrophotometer (Kaiao, Beijing, China). The RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 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.
RNA-seq:A total amount of 3 ?g RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Epicentre Ribo-Zero? Gold Kits(Human/Mouse/Rat) (Epicentre, USA). Subsequently, the sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra? Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) . ATAC-seq: The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 ?L. 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 RNA-seq: The fastq files generated by the Illumina workflow underwent read-level quality control before mapping, using FastQC (v0.11.4). For sample with poor read quality, quality trimming was performed using Trim Galore (v0.4.4, Quality Phred score cut-off: 30).The HISAT2 (v2.0.5, default parameters) was utilized for mapping the reads with the Mmul 8.0.1 reference genome and the Mmul transcriptomic annotation GTF. Read counts of genes were generated using HTSeq (v0.6.1).
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. UCSC bedGraphToBigWig was used to generate bigWig files. Peak calling was performed with MACS2 (v2.1.0.20151222) using parameters ?--nomodel --nolambda --shift 100 --extsize 200 -B --SPMR?.
Genome_build: Mmul 8.0.1
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample; bigwig
Submission date Mar 19, 2019
Last update date Dec 31, 2019
Contact name keying Lu
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
BioSample SAMN11167193
SRA SRX5543756

Supplementary file Size Download File type/resource 342.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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