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| Status |
Public on Mar 11, 2020 |
| Title |
H3K27ac_ChIPSeq_VEH 3_PND5 |
| Sample type |
SRA |
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| Source name |
Rat liver
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| Organism |
Rattus norvegicus |
| Characteristics |
chip antibody: H3K27ac (Abcam, ab4729)
strain: Sprague Dawley
treatment: Sesame oil (VEH)
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| Treatment protocol |
Neonatal rats were treated with vehicle (VEH; sesame oil) or bisphenol A (BPA; 50 µg/kg dissolved in sesame oil) orally via pipette tip on post-natal days 1, 3, and 5. Littermates of the same sex were randomly assigned to the treatment groups. BPA was obtained from the National Instutite of Environmental Health Sciences (NIEHS). The dose and route of administration recapitulates human exposure to BPA. Rats were fasted overnight prior to tissue collection.Liver tissue was harvested on post-natal day 5 at 6 hours after treatment (PND5), and on day 70 (D70). Tissue was snap-frozen in liquid nitrogen for downstream epigenomic analyses.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen liver tissue was pulverized, followed by cross-linking of proteins to DNA with 37% formaldehyde, and then incubation with 10X glycine to stop the reaction. Cross-linked tissue was homogenized, and centrifuged at 1,500 rpm for 5 min at 4°C. The cell pellet was resuspended with cell lysis buffer (PBS with 0.5 mM EDTA and 0.05% Triton X-100), incubated on ice for 15 min, followed by centrifiugation at 5,000 rpm for 5 min at 4°C. The cell pellet was then resuspended with nuclear lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl at pH 8.1) and incubated on ice for 10 min. Chromatin was sonicated with a bioruptor (Diagenode, Denville, NJ) to obtain fragment sizes of 100-300 bp for ChIP-seq. ChIP was performed by incubating sheared chromatin with Magna ChIPTM Protein A+G magnetic beads, and antibodies against H3K4me3, H3K4me1, H3K27ac or H3K27me3 overnight at 4°.The next day, the beads were washed with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 150 mM NaCl) high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 500 mM NaCl), lithium chloride wash buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl pH 8), and TE buffer (20 mM Tris-HCl pH 8 and 1 mM EDTA) for 5 minutes each at 4°. Immunoprecipitated DNA was recovered from the beads by incubation with ChIP elution buffer (1% SDS, 1 mM EDTA, 50 mM NaHCO3, and 50 mM Tris-HCl pH 8) and proteinase K for 2 hours at 62° with shaking, followed by incubation at 95° for 10 minutes. DNA was purified using the QIAquick PCR Purification kit (Qiagen) and DNA concetration was measured using a NanoDrop spectrophotometer (Thermo Scientific).
Sequencing librairies were prepared using Bioo Kit Option 2 protocol using 1.7-10 ng of DNA per sample.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the rat genome build UCSC rn6 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Differential regions were determined using the diffReps software using the G-test with significance achieved for a fold change > 2 and an FDR-adjusted q-value < 0.01.
Genome_build: rn6
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in WIG and TDF format
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| Submission date |
Apr 28, 2019 |
| Last update date |
Mar 11, 2020 |
| Contact name |
Cheryl L Walker |
| E-mail(s) |
cheryl.walker@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Department |
Center for Precision Environmental Health
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| Street address |
1 Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (2) |
| GSE130409 |
Genome wide anaylsis of histone modifications in rats exposed to endocrine disruptors. [ChIP-Seq] |
| GSE130436 |
Genome wide anaylsis of rats exposed to endocrine disruptors. |
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| Relations |
| BioSample |
SAMN11522733 |
| SRA |
SRX5761710 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3738076_trim.Sample_29_VEH_3_K27ac.signals.tdf |
63.8 Mb |
(ftp)(http) |
TDF |
| GSM3738076_trim.Sample_29_VEH_3_K27ac.signals.wig.gz |
14.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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