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Sample GSM2054568

Query DataSets for GSM2054568

Status

Public on Oct 20, 2016

Title

GZ, individual 2

Sample type

SRA

Source name

Fetal brain

Organism

Homo sapiens

Characteristics

developmental stage: Postconception week 18
tissue: Fetal cortex
layers: Germinal zone

Extracted molecule

genomic DNA

Extraction protocol

Fetal brains dissected into cortical plates (CP) and germinal zone (GZ).
Tissue was fixed in 1% formaldehyde for 10 min. Cross-linked DNA was digested by restriction enzyme HindIII. Digested chromatin ends were filled and marked with biotin-14-dCTP. Resulting blunt-end fragments were ligated under dilute concentration to minimize random intermolecular ligations. DNA purified after crosslinking was reversed by proteinase K treatment. Biotins from unligated ends were removed by exonuclease activity of T4 DNA polymerase. DNA was sheared by sonication and 300-600bp fragments were selected. Biotin-tagged DNA, which is intermolecular ligation products, was pulled down with streptavidin beads (Invitrogen, 65001), and ligated with Illumina paired end adapters. Resulting Hi-C library was amplified by PCR and sequenced by Illumina 50bp paired-end sequencing.

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 2000

Description

processed data file: FBP_IC-heatmap-chr-10k.hdf5
processed data file: FBP_IC-heatmap-chr-40k.hdf5
processed data file: FBP_IC-heatmap-res-100k.hdf5
processed data file: Sczloci_interacting_region_FBP_FDR.bed
processed data file: Evolloci_interacting_region_enhctrl_FBP_FDR.bed

Data processing

Library strategy: Hi-C
alignment: bowtie2 (--score-min -L 0.6,0.2--very-sensitive)
filtering and bias correction: hiclib
normalization: hiclib
Genome_build: hg19
Supplementary_files_format_and_content: *hdf5 files contain a normalized chromatin contact matrix at different resolutions, included in file name (10kb, 40kb, 100kb); Sczloci*.bed files contain schizophrenia GWAS loci interacting regions, and Evolloci*.bed files contain Human-gained enhancer interacting regions; CP_TAD.bed file contains TAD coordinates in bed file format for CP (cortical plate); GZ_TAD.bed contains TAD coordinates in bed file format for GZ (germinal zone).

Submission date

Feb 03, 2016

Last update date

Feb 22, 2021

Contact name

Hyejung Won

E-mail(s)

hyejung_won@med.unc.edu

Phone

3106000592

Organization name

UNC