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| Status |
Public on May 30, 2018 |
| Title |
Gibbon_H3K4me3_rep1 |
| Sample type |
SRA |
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| Source name |
Lymphoblasts
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| Organism |
Nomascus leucogenys |
| Characteristics |
cell type: EBV-transformed cell line
chip antibody: anti-H3K4me3
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| 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Chromatin
processed data file: NLE-ChIP-H3K4me3-final-peaks.bw
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| 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.
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| Submission date |
May 29, 2018 |
| Last update date |
May 30, 2018 |
| Contact name |
Lucia Carbone |
| E-mail(s) |
carbone@ohsu.edu
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| Organization name |
Oregon Health & Science University
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| Street address |
3303 SW Bond Ave.
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| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN09279559 |
| SRA |
SRX4138633 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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