|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jul 01, 2024 |
Title |
U2OS-KRAB-IDR3-TCF3, H3K9me3, ABCAM, rep2 |
Sample type |
SRA |
|
|
Source name |
U2OS
|
Organism |
Homo sapiens |
Characteristics |
cell line: U2OS cell type: Human Bone Osteosarcoma Epihelial Cells chip antibody: H3K9me3 (Abcam, #ab8898)
|
Growth protocol |
DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were washed in FBS-free media then cross-linked with 1% formaldehyde for 10 min at room temperature, Cross-linked cells were washed with ice-cold PBS, For each sample, 20 million fixed cells were lysed to prepare nuclear extracts. For ChIP-Seq, 5ng of purified ChIP DNA were used to generate the sequencing library using a NEB kit and sequenced with the Illumina HiSeq X Ten.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
IP_2_peaks.broadPeak
|
Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, using Trimgalore v0.6.7, discarding reads left with < 30 bp ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie2 version 2.5.0. Only uniquely mapping reads with were retained. To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were renormalized (to reads per million, rpm) and reformatted in the bigWig file format. Peaks were called uing MACS v2.2.7.1 with the significance cut-off p-value <=0.01 Assembly: hg19 Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
|
|
|
Submission date |
Mar 20, 2023 |
Last update date |
Jul 01, 2024 |
Contact name |
YING FENG |
E-mail(s) |
fengying@mail.ecust.edu.cn
|
Organization name |
Shanghaitech University
|
Street address |
393 Middle Huaxia Road
|
City |
Shanghai |
ZIP/Postal code |
201210 |
Country |
China |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE227780 |
The Local Density of H3K9me3 Dictates The Stability of HP1a Condensates-mediated Genomic Interactions |
|
Relations |
BioSample |
SAMN33833090 |
SRA |
SRX19734333 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7108086_R22037393IP_2_KRAB_IDR3_TCF3_R1_unique.bw |
153.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
|
|
|
|
|