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| Status |
Public on Oct 01, 2021 |
| Title |
BAN129 |
| Sample type |
SRA |
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| Source name |
whole body
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| Organism |
Caenorhabditis elegans |
| Characteristics |
age: L4
strain: nuo-6(qm200); his-72p::his-72::gfp
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| Growth protocol |
worms bleached onto OP50-seeded NGM plates and allowed to reach the L4 stage
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Worms were collected in M9, snap frozen and stored at -80°C. Chromatin extracted as previously described (Askjaer, P., et. al. Modern techniques for the analysis of chrmatin and nuclear organization in C. elegans (April 2, 2014), WormBook, et. The C. elegans Research Community, Woembook, doi/10.1895/wormbook.1.169.1, http://wormbook.org
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. 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.
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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 |
Peaks were called using either the MACS or SICER algorithms
MACS default cutoff is pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks, and SICER default cutoff is FDR 1e-10 with gap parameter of 600 bp
Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.
Genome_build: WS220/ce10
Supplementary_files_format_and_content: bigwig files, which contain both the signal map and peak metrics, and can be opened with genome browsers.
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| Submission date |
Mar 08, 2021 |
| Last update date |
Oct 01, 2021 |
| Contact name |
Daniele Bano |
| Organization name |
DZNE
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| Street address |
Sigmund-Freud-Strasse 27
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| City |
Bonn |
| ZIP/Postal code |
53127 |
| Country |
Germany |
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| Platform ID |
GPL19757 |
| Series (2) |
| GSE168500 |
CEST-2.2 stimulates lipid metabolism and promotes longevity in mitochondrial mutant animals (ChIP-Seq) |
| GSE168502 |
CEST-2.2 stimulates lipid metabolism and promotes longevity in mitochondrial mutant animals |
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| Relations |
| BioSample |
SAMN18210913 |
| SRA |
SRX10274854 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5144819_5_01VP_006SDZNE_BAN129_GFP_ce10_i91_uniqnorm_signal.bw |
11.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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