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Sample GSM3164323 Query DataSets for GSM3164323
Status Public on May 30, 2018
Title Gibbon_input
Sample type SRA
 
Source name Lymphoblasts
Organism Nomascus leucogenys
Characteristics cell type: EBV-transformed cell line
chip antibody: none
Extracted molecule genomic DNA
Extraction protocol EBV-transformed cells were cross-linked and lysed with Lysis buffer (0.1% SDS, 0.5% Triton X-100, 20mM Tris-HCl pH 8.0, 150mM NaCl and protease inhibitor cocktail). Lysate was sheared using the Bioruptor sonicator until the lysate was cleared. Lysate was incubated with 1ug of anti-H3K4me3 antibody (Abcam, ab8580). Prepared Pierce Protein A/G Magnetic Beads (Thermo Fisher Scientific) were added to lysates, incubated for 2 hour at 4°C and then washed four times with TBST (25mM Tris-HCl pH 7.6, 250mM NaCl, 0.05% Tween-20), once with LiCl Wash Buffer (10mM Tris-HCl pH 8.0, 0.5M LiCl, 1mM EDTA, 0.05% Tween-20), once with Lysis Buffer and once with 1X TE. Elution reactions were pooled and incubated with NaCl overnight at 65°C to reverse crosslinks. The elution product was used to generate libraries.
Libraries were constructed using NEBNext Ultra II DNA Library preparation Kit (NEB, E7645S).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description Chromatin
processed data file: NLE-ChIP-H3K4me3-final-peaks.bw
Data processing Removed adapter using Trimmomatic.
De-duplicated reads using fastx-toolkit v0.0.13.
Mapped to the reference genome using BWA-mem v0.7.9a.
Used phantompeakqualtools v2.0 to run SPP to obtain a loose set of peaks.
Performed an irreproducibility discovery rate (IDR) analysis using ENCODE guidelines.
Genome_build: Nleu3.0
Supplementary_files_format_and_content: NLE-ChIP-H3K4me3-final-peaks.bw: bigWig tracks of final H3K4me3 ChIP-seq peaks.
 
Submission date May 29, 2018
Last update date May 30, 2018
Contact name Lucia Carbone
E-mail(s) carbone@ohsu.edu
Organization name Oregon Health & Science University
Street address 3303 SW Bond Ave.
City Portland
State/province Oregon
ZIP/Postal code 97239
Country USA
 
Platform ID GPL25055
Series (2)
GSE115064 Epigenetic maintenance of topological domains in the rearranged gibbon genome [ChIP-seq]
GSE115065 Epigenetic maintenance of topological domains in the rearranged gibbon genome
Relations
BioSample SAMN09279557
SRA SRX4138635

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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