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Sample GSM3384085

Query DataSets for GSM3384085

Status

Public on Feb 18, 2019

Title

Hi-C_PS_bio1

Sample type

SRA

Source name

Pachytene spermatocytes

Organism

Mus musculus

Characteristics

strain: C57BL/6J
source tissue: Testis
cell type: Pachytene spermatocytes
number of mice: ≥12
age: 90-120 days
genotype: wild type

Extracted molecule

genomic DNA

Extraction protocol

Pachytene spermatocytes and round spermatids were isolated from adult testes through sedimentation velocity at unit gravity as described (PMID 8231890). At least 12 independent mice, 90-120 days in age, were used for each isolation of germ cells. Wet lab procedures for Hi-C were performed as described (PMID 28435001), and samples were treated with HindIII restriction enzyme.
Hi-C library construction was performed as described (PMID 28435001) with the following detail: For DNA sequencing, NEBNext Oligos for Illumina, Index Primer Set 1, were used.

Library strategy

Hi-C

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 4000

Description

PS_pooled_validpairs.txt.gz
PS_pooled.mcool

Data processing

Libraries were sequenced on Illumina HiSeq2500 or HiSeq4000 machines following the manufacturer's instructions. Bases were called using Illumina's HiSeq Control Software.
Paired-end .fastq files of Hi-C libraries were mapped and processed using the cMapping package (https://github.com/dekkerlab/cMapping).
Hi-C reads were iteratively mapped to the Mus musculus mm10 genome via Bowtie2 (version 2.3.3.1), which was called with the following arguments: --very-sensitive --no-head --no-sq --qc-filter --reorder.
Uniquely aligned, paired reads were kept and assigned to the 5’ position of HindIII restriction fragments.
Mapped reads were filtered for fragment ends and uniqueness; PCR duplicates, defined as sequence matches with the exact same start and end, were excluded.
Using the cooler package (version 0.7.10; https://github.com/mirnylab/cooler), valid pairs pooled from biological replicates (in validpairs.txt.gz files) were binned at multiple resolutions (resulting in .mcool files).
To correct for noisy and/or low-signal bins prior to matrix balancing with cooler, bins whose log marginal sum is less than ≤20 genome-wide median absolute deviations below the median log marginal sum of all the bins in the same chromosome were excluded.
Matrices were balanced using Sinkhorn balancing such that the sum of every row and column is equal.
Genome_build: mm10
Supplementary_files_format_and_content: validpairs: Tab-delimited text files listing valid interacting pairs of Hi-C reads; mcool: A file containing chromosome interractions, made from the validPairs files, binned at multiple resolutions (kb) as follows: 1, 2, 5, 8, 10, 15, 20, 30, 40, 64, 100, 128, 250, 256, 512, 1024, 2048, 4096, and 8192.

Submission date

Sep 11, 2018

Last update date

Feb 18, 2019

Contact name

Satoshi H Namekawa

E-mail(s)

satoshi.namekawa@cchmc.org

Phone

513-803-1377

Organization name

Cincinnati Children's Hospital Medical Center