|
| Status |
Public on Dec 07, 2017 |
| Title |
ChIP-Seq: SMC3 WAPL-depleted rep2 |
| Sample type |
SRA |
| |
|
| Source name |
cervical carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HeLa Kyoto
RNAi: Wapl RNAi
genotype: Wapl-depleted
chip antibody: SMC3
|
| Growth protocol |
HeLa Kyoto cells were synchronized at G1, S, G2, or in ProMeta-Phase.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
ChIP as well as Hi-C libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
union of 2 replicates, p-val. threshold 1e-10 each
|
| Data processing |
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup_v0.5.8
bowtie-align version 1.2.1.1
truncating, mapping, filtering and deduplicating of Hi-C raw data with hicup.
ChIP-seq: Bowtie 0.12.5 and 1.0.0 for ChIP-Seq readmapping, reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq MACS peak calling version 1.4.2
Genome_build: hg19
Supplementary_files_format_and_content: juicer tools derived .hic files (Aiden Lab) containing Hi-C matrices for usage with juicebox and juicer tools for Hi-C, and wiggle resp. bed files for ChIP-Seq data
Supplementary_files_format_and_content: wig files were generated using MACS 1.4.2 with output switches [-w -S] and represent genomic distribution of the factors as described in the paper.
|
| |
|
| Submission date |
Aug 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Roman R Stocsits |
| E-mail(s) |
roman.stocsits@imp.ac.at
|
| 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 |
GPL11154 |
| Series (1) |
| GSE102884 |
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL and PDS5 proteins |
|
| Relations |
| BioSample |
SAMN07524523 |
| SRA |
SRX3110773 |
