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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 11, 2021 |
| Title |
Input-pooled |
| Sample type |
SRA |
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| Source name |
heart tissue
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| Organism |
Mus musculus |
| Characteristics |
strain and age: C57/Bl/6J - 12 wk-old
diet: pooled
Sex: male
surgical procedure: Sham
antibody: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted from heart tissue, sonicated, and histone-DNA complexes were precipitated with anti-H3K9Bu or anti-H3K9ac (a pool of 3, each)
Library was constructed by Active Motif (https://www.activemotif.com/)
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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 |
The 75-nt single-end (SE75 sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm (“bwa aln/samse” with default settings)
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´- ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected library. To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers (see Section VI.). bigWig files also provide the peak metrics in the Active Motif analysis program described below.
Peak finding was performed using SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files - Binary files that can be opened in or uploaded to genome browsers and show the fragment density for 32-nt bins along the genome (“signal map”).
Supplementary_files_format_and_content: MERGED (PEAK) REGIONS – an 'excel' file comparing peak region metrics between different samples
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| Submission date |
Jan 21, 2021 |
| Last update date |
May 11, 2021 |
| Contact name |
Maha Abdellatif |
| E-mail(s) |
abdellma@njms.rutgers.edu
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| Phone |
9739721254
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| Organization name |
Rutgers-University
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| Department |
Cell Biology and Molecular Medicine
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| Street address |
185 S. Orange Ave.
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| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07103 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE165284 |
ACAA2 genome-binding patterns before and after transverse aortic constriction in C57Bl/6J mice on different diets [ACAA2] |
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| Relations |
| BioSample |
SAMN17487058 |
| SRA |
SRX9912262 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5029410_00_06U5_00VWRutgers_Pooled_Input_mm10_i43_uniqnorm_signal.bw |
176.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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