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| Status |
Public on Oct 25, 2023 |
| Title |
XL177, Smc3 ChIP-Seq |
| Sample type |
SRA |
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| Source name |
XL177
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| Organism |
Xenopus laevis |
| Characteristics |
cell line: XL177
cell type: immortalized non-epidermal epithelial cell line
antibody: anti-Smc3 (Bethyl, A300-060A)
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| Treatment protocol |
No treatment was applied to XL177 cells. Some of the pronuclei samples were treated by adding recombinant CTCF protein.
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| Growth protocol |
Xenopus laevis XL177 cells were cultured at 16-20º C in medium containing 65% Leibovitz’s L-15 (Thermo Fisher Scientific, #11415064), 15% FBS (Gibco, 10270106), 20% H2O, 100 U/ml Penicillin and 100 µg/ml Streptomycin (Sigma, P0781). Pronuclei were generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. After quenching with glycine and cell lysis with SDS, chromatin was sonicated using a Bioruptor sonication device.
ChIP was performed as previously described (Wendt et al., Nature 2008), and the following antibodies were used: anti-Smc3 (Bethyl, A300-060A), anti-CTCF (Millipore, 07-729). The DNA samples were submitted for library preparation and Illumina deep sequencing on HiSeq 2500 SR50 to the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria.
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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 |
Basecalling software: Illumina RTA
ChIP-seq reads were mapped uniquely with 0 to 2 errors against the Xenopus laevis v9.2 genome as well as the Mus musculus mm9 genome assembly using bowtie version 1.2.2.
Peaks were called using the intersection of the peaks called using MACS version 1.4.2 with an assumed mappable genome size of 2.5e9 and a p-value threshold of 1e-10, and MACS v2.2.5 with default parameters.
TDF files for IGV and Juicebox browsers were generated from wig files using igvtools toTDF
bedGraph files (*.bedGraph) have been built using MACS v2.2.5 with -B option
Assembly: Xenopus laevis v9.2, mm9
Supplementary files format and content: bedGraph files for ChIP-Seq signal distributions represent genomic distribution of the factors as described in the paper, they can be used for visualization in IGV and Juicebox browsers
Supplementary files format and content: bed files describe genomic location and can be used as coordinates and for visualization in IGV and Juicebox browsers
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| Submission date |
Jul 11, 2023 |
| Last update date |
Oct 25, 2023 |
| Contact name |
Roman R Stocsits |
| E-mail(s) |
roman.stocsits@imp.ac.at
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| Organization name |
IMP - Research Institute of Molecular Pathology
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| Lab |
Jan-Michael Peters' Lab
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| Street address |
Campus-Vienna-Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL18936 |
| Series (2) |
| GSE237049 |
Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei |
| GSE237051 |
Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei |
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| Relations |
| BioSample |
SAMN36405530 |
| SRA |
SRX20980260 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7593931_XL177_SMC3_65467.macs2.2023_treat_pileup.bedGraph.gz |
298.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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