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Sample GSM2940124 Query DataSets for GSM2940124
Status Public on Feb 11, 2019
Title RNA_monkey_fibroblast_rep2
Sample type SRA
 
Source name fibroblast
Organism Macaca mulatta
Characteristics cell type: fibroblast
Extracted molecule genomic DNA
Extraction protocol The RNA extraction follows smart-seq2 protocol
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously with minor modification (Picelli et al., 2014). Cells were lysed in hypotonic lysis buffer (Amresco, M334), and the polyadenylated mRNAs were captured by the PolyT primers. After ~3–10 min lysis at 72 °C, the Smart-seq2 reverse transcription reactions were performed. After pre-amplification and AMPure XP beads purification, cDNAs were sheared by Covaris and were subject to Illumina TruSeq library preparation. All libraries were sequenced on Illumina HiSeq 2500 according to the manufacturer’s instruction.
 
Library strategy RNA-Seq
Library source genomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description monkey_fibro_pac_rs_gene.fpkm.txt.gz
Data processing Basecalls performed using CASAVA version 1.8
For Hi-C sapples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For methylation samples: STEM-seq reads were aligned to the rheMac2 genome using BSseeker2.0.8, and methylation value in bedGraph files were counted by the number of reads falling into 200bp bin in the genome.
For RNA-seq samples: SMART-seq2 reads were aligned to the rheMac2 or mm9 genome assembly using tophat2 version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: rheMac2, mm9
Supplementary_files_format_and_content: The bedgraph files contains the values counted by the number of reads falling into 200bp bin in the genome. The gene fpkm txt file contains FPKM value for all samples. with number for each bin. While the validpair txt file indicates the paired interaction reads for each sample.
 
Submission date Jan 18, 2018
Last update date Feb 11, 2019
Contact name Wei Xie
E-mail(s) xiewei121@tsinghua.edu.cn
Organization name Tsinghua University
Street address Zhongguancun north street
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL24522
Series (1)
GSE109344 Reprogramming of meiotic chromatin architecture during primate spermatogenesis
Relations
BioSample SAMN08375212
SRA SRX3591106

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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