|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jan 23, 2014 |
Title |
BMI1_CST_Scr_ChIPSeq |
Sample type |
SRA |
|
|
Source name |
DU145 prostate cancer cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: DU145 prostate cancer cells genotype/variation: control chip antibody: Anti-BMI1 [rabbit, Cell Signaling, cat# 6964, lot# 1]
|
Treatment protocol |
stable cells were selected with puromycin
|
Growth protocol |
Du145 cells were growth following ATCC instruction
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. ChIP was performed using HighCell ChIP kit following manufacturers protocol (Diagenode) ChIP-Seq libraries were prepared using standard Illumina protocol. ChIP-enriched DNA samples (10-20 ng) were converted to blunt-ended fragments using a combination of T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3' to 5' exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina PE1.0/PE2.0 primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified using the Bioanalyzer 2100 (Agilent) and each sample was sequenced in a single lane on the Illumina HiSeq 2000 (40 nucleotide read length).
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
Scramble
|
Data processing |
Illumina Casava1.7 software used for basecalling. ChIP-seq reads were aligned to the hg19 genome assembly using bowtie with up to 3 mismatches peaks were called using HPeak version 3 with the following setting: 25 bp window, 1e-3 significant level, using pair-end setting with dynamic fragment length Genome_build: hg19 Supplementary_files_format_and_content: Tab-delimited text files were generated using HPeak ver. 3, which provided peak loci, height, width, summit location and log(p-value)
|
|
|
Submission date |
May 09, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Meng Zhao |
E-mail(s) |
meng.zhao@emory.edu
|
Phone |
404-712-8611
|
Organization name |
Emory University
|
Department |
BIOS
|
Lab |
Steve Qin
|
Street address |
1518 Clifton Rd, #369
|
City |
Atlanta |
State/province |
GA |
ZIP/Postal code |
30322 |
Country |
USA |
|
|
Platform ID |
GPL9115 |
Series (1) |
GSE42566 |
The Central Role of EED in the Orchestration of Polycomb Group Complexes |
|
Relations |
BioSample |
SAMN02141775 |
SRA |
SRX276784 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1138594_BMI1.CST.Scr.HPeak.txt.gz |
339.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|