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Sample GSM4974119

Query DataSets for GSM4974119

Status

Public on Dec 15, 2020

Title

RM02_GZ_RNA-seq

Sample type

SRA

Source name

Brain

Organism

Macaca mulatta

Characteristics

tissue: Brain
developmental stage: E84
genotype: wild type

Extracted molecule

total RNA

Extraction protocol

RNA was extracted from GZ and CP cells using the QIAGEN miRNeasy Mini Kit (Qiagen, 217004).
2 ug total RNA were used to generate the cDNA libraries, respectively, according to TruSeq RNA Sample Prep Kit protocol.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

monkey-RNASeq-cqnnormalized-FPKM-log2-matrix.txt

Data processing

Hi-C:Paired-end reads of the Hi-C libraries were pre-processed using HiC-Pro. In brief, reads pairs were aligned to the reference genomes ( rheMac8 ) in two steps. The first step aligns reads using bowtie2 end-to-end algorithm. The second step detect the ligation sites and the 5’ fraction of the reads were aligned back to the genome. Aligned read pairs were assigned to DpnII restriction fragments. Invalid pairs like dangling end were filtered out. The genome was divided into specific size bins, and valid pairs were counted per bins. We used 500 kb, 100 kb, 40 kb bin sizes to generate raw and ICE or KR normalized matrix.
RNA-seq:The intra-species RNA-Seq Fastq reads were aligned to Mmul_8.0.1 reference genome using STAR. ENSEMBL gene annotation was used. Duplicated alignments were removed using PicardTools. The number of alignments mapped to exons was counted using the summarizeOverlap func-tion from the GenomicAlignments package. Condi-tional quantile normalization was performed using CQN package to correct read depth, exon length and GC content. Log2 normalized FPKM was used for quantification of expression levels.
ChIP-seq:The Fastq reads were aligned to reference genome (rheMac8) using bowtie2 with settings “bowtie2 –very-sensitive”. Bam files were transferred to sam files using Samtools. Duplicated alignments were removed using PicardTools. To avoid double contigs for the paired-end alignments, only one mate count. Only uniquely mapped alignments (MAPQ > 30) were kept. Averaged reads per million of mapped reads (RPM) in 10bp bins were calculated by deepTools and transferred to coverage tracks. Technical replicates data were merged. Peaks were identified using MACS2 (for CTCF ChIP-seq) with settings “macs2 call Peak –B –p 1e-5 –nomodle –extsize 200” or HOMER (for DNase-seq) with setting "-size 147 -gsize 2.7e09 -norm 1000000 -fragLength 147 -fdr 0.01 -style factor".
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: Hi-C: (1) .hic files represent all the valid paris per sample and can be used for further analysis
Supplementary_files_format_and_content: (2) .bed files represent all the boundaries per sample generated by insulation score method
Supplementary_files_format_and_content: (3) .bedpe files represent all the loops per sample generated by HICCUPS
Supplementary_files_format_and_content: RNA-seq: matrix table text file represent the log2 FPKM value per sample
Supplementary_files_format_and_content: ChIP-seq: (1) .bw files represent the reads distribution
Supplementary_files_format_and_content: (2). txt files represent deteced peaks using MACS2 or HOMER

Submission date

Dec 14, 2020

Last update date

Dec 19, 2020

Contact name

Yuting Liu

E-mail(s)

lyt17@pku.edu.cn

Organization name

Peking University

Department

School of Life Science