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Sample GSM7593931 Query DataSets for GSM7593931
Status Public on Oct 25, 2023
Title XL177, Smc3 ChIP-Seq
Sample type SRA
Source name XL177
Organism Xenopus laevis
Characteristics cell line: XL177
cell type: immortalized non-epidermal epithelial cell line
antibody: anti-Smc3 (Bethyl, A300-060A)
Treatment protocol No treatment was applied to XL177 cells. Some of the pronuclei samples were treated by adding recombinant CTCF protein.
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.
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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
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
Submission date Jul 11, 2023
Last update date Oct 25, 2023
Contact name Roman R Stocsits
Organization name IMP - Research Institute of Molecular Pathology
Lab Jan-Michael Peters' Lab
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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