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| Status |
Public on Dec 15, 2024 |
| Title |
ChIP_XerA_input_KU216_rep2 |
| Sample type |
SRA |
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| Source name |
KOD1
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| Organism |
Thermococcus kodakarensis |
| Characteristics |
cell line: KOD1
strain: Parental strain KU216
chip antibody: None
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked cells were lysed by sonication, and the extract was clarified by centrifugation. Protein-DNA complexes were purified from the extract with antisera. After reversal of crosslinks, the DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated in ethanol.
Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Data were mapped using Bowtie 2 version 2.3.5.1 (Langmead & Salzberg, 2012). Low-quality alignments (MAPQ < 30) were removed using SAMtools version 1.9 (Li et al., 2009). Generated BAM files were processed using the bamCoverage function (version 3.5.1) of deepTools (Ramirez et al., 2016) to calculate Reads Per Kilobase region per Million mapped reads (RPKM) for genomic bins. Mapped data were processed for peak calling using MACS v3.0.0a6 with the following setting: --fe-cutoff 3, --keep-dup all, --call-summits, -m 1 50.
Assembly: GCA_000009965.1
Supplementary files format and content: bedgraph
Supplementary files format and content: bed
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| Submission date |
Jun 18, 2024 |
| Last update date |
Dec 15, 2024 |
| Contact name |
Naomichi Takemata |
| Organization name |
Kyoto University
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| Department |
Synthetic Chemistry and Biological Chemistry
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| Street address |
Kyoto University, Katsura, Nishikyo-ku
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| City |
Kyoto |
| ZIP/Postal code |
615-8510 |
| Country |
Japan |
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| Platform ID |
GPL28196 |
| Series (1) |
| GSE267298 |
Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [ChIP-seq] |
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| Relations |
| SRA |
SRX24972796 |
| BioSample |
SAMN41900429 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8337647_ChIP_XerA_input_KU216_rep2.bedgraph.gz |
284.9 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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