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Sample GSM1563749 Query DataSets for GSM1563749
Status Public on Jul 25, 2016
Title HeLa-S3_LATS2-/-_H3K27ac_ChIPSeq
Sample type SRA
Source name LATS2-knockout HeLa-S3 cells
Organism Homo sapiens
Characteristics cell line: HeLa-S3
tissue: cervix
genotype: LATS2-/-
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP DNA and input DNA ends were repaired using T4 DNA polymerase, Klenow enzyme, and T4 polynucleotide kinase (PNK) (New England Biolabs), followed by treatment with Klenow exo- to add an A base to the 3′-end. After ligation of the Genomic Adaptor Oligo Mix (Illumina) using TaKaRa Ligation Mix (TaKaRa), the adaptor-ligated DNA fragments were amplified with Paired-End Sample Prep Oligo primers (Illumina) for 18 cycles. The amplified library was separated on a 2.0% agarose gel, and the samples were purified using the QIAquick MinElute kit (Qiagen) after each preparation step. The purified library was used for cluster generation and sequencing analysis on a HiSeq 2000 (Illumina)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description KO_H3K27ac_ChIPSeq
Data processing The MACS software (ver. 1.4.1) was used for peak detection of each histone mark. The parameters for MACS were ‘--nomodel --extsize 146 --broad --to-large --pvalue 1e-3’, and the other parameters were the software defaults.
Genes were called in association with a given chromatin mark only when peaks were called within ±5 kb of the TSS.
To calculate normalized depth around TSSs of all RefSeq genes, and to perform GO analysis of the called genes, the Homer software was used with the default settings.
To visualize normalized ChIP profiles in genome browser, BigWig files were generated using our custom scripts and visualized using the IGV software from the Broad Institute.
Genome_build: Sequence reads for H3K27me3, H3K4me3, and input were aligned to the human genome (hg19) using the Bowtie software (parameter: -v 3 –m 1)
Supplementary_files_format_and_content: bigWig files were generated for processed data containing chromosome, regions
Submission date Dec 11, 2014
Last update date May 15, 2019
Contact name Daisuke Okuzaki
Phone +81-6-6879-4935
Organization name Osaka univ.
Department Immunology Frontier Research Center
Lab Human Immunology (Single Cell Genomics)
Street address Yamadaoka 3-1
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
Platform ID GPL11154
Series (2)
GSE63538 LATS2 regulates repressive epigenetic integrity via regulation of Polycomb repressive complex 2
GSE64072 Genome-wide maps of chromatin state in LATS2-knockout HeLa-S3 cell
BioSample SAMD00021088
SRA DRX022426

Supplementary file Size Download File type/resource 20.7 Mb (ftp)(http) BW 26.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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