|
| Status |
Public on Jul 25, 2016 |
| Title |
HeLa-S3_LATS2-/-_H3K4me3_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_H3K4me3_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 |
| E-mail(s) |
dokuzaki@biken.osaka-u.ac.jp
|
| 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 |
|
| Relations |
| BioSample |
SAMD00021088 |
| SRA |
DRX022428 |
