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Sample GSM2940099

Query DataSets for GSM2940099

Status

Public on Feb 11, 2019

Title

Hi-C_monkey_fibroblast_rep1

Sample type

SRA

Source name

fibroblast

Organism

Macaca mulatta

Characteristics

cell type: fibroblast

Extracted molecule

genomic DNA

Extraction protocol

The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
TruSeq

Library strategy

Hi-C

Library source

genomic

Library selection

other

Instrument model

HiSeq X Ten

Description

monkey_fibroblast_rep12_allValidPairs.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