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| Status |
Public on Apr 12, 2017 |
| Title |
sham_1d_HNF |
| Sample type |
SRA |
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| Source name |
liver from animals with sham surgery, 1 day after surgery
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| Organism |
Rattus norvegicus |
| Characteristics |
surgery: sham
time following surgery(d): 1
chip antibody: HNF (Santa Cruz Biotechnology sc-8986)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were aligned to the rat genome (rn5) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality ≥ 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
Peak locations were determined using the MACS algorithm (v1.4.2; parameters used were --gsize=2e9 --bw=200 --mfold=12,32 --pvalue=1e-07).
Genome_build: rn5.1
Supplementary_files_format_and_content: Bigwig files were generated using the BWA algorithm.The resulting files show the fragment density for 32-nt bins along the genome (“signal map”). The files can be uploaded to the UCSC browser.
Supplementary_files_format_and_content: Peak files were generated using the MACS algorithm.
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| Submission date |
Oct 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Keith M Goldstein |
| E-mail(s) |
goldsteinkm@lilly.com
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| Organization name |
Eli Lilly & Co.
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| Department |
Investigative Toxicology
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| Lab |
Keith Goldstein
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| Street address |
Lilly Corporate Center
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| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46285 |
| Country |
USA |
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| Platform ID |
GPL20084 |
| Series (1) |
| GSE87730 |
Toxicogenomic module associations with pathogenesis: A network based approach to understanding drug toxicity (ChIP-Seq) |
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| Relations |
| BioSample |
SAMN05877139 |
| SRA |
SRX2226583 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2339396_08_rnliver_sham-24hr_HNF-1_i74_uniq_signal.bw |
88.5 Mb |
(ftp)(http) |
BW |
| GSM2339396_08_sham-24hr_HNF-1_peaks.xls.gz |
168.6 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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