|
Status |
Public on Apr 05, 2017 |
Title |
KD1_H3K27ac |
Sample type |
SRA |
|
|
Source name |
Endometriosis
|
Organism |
Homo sapiens |
Characteristics |
cell type: hTERT immortalized endometriosis cells genotype/variation: ARID1A Knockdown antibody: H3K27ac
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Nuclei were fixed, lysed, and chromatin was sonicated. Histone-DNA complexes were isolated with antibody. Genomic DNA was isolated by standard phenol-chloroform extraction and ethanol precipitation Libraries were prepared according to Illumina's instructions and sequenced on either HiSeq-2000 or NextSeq 500 platforms.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations… Non-unique reads were filtered out and reads were mapped to hg19 using BWA Reads were extended to 200bp, duplicates removed. Peaks were called using MACS algorithm with a p-value cut-off of 10^-10. Read-count quantification was perfomed then log2 transformed -- corrected for total read count of the largest datastore, only reads within peaks were counted, and corrected for peak length. Genome_build: hg19 Supplementary_files_format_and_content: Text files with peak list and read-count quantification
|
|
|
Submission date |
Sep 12, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Ranjani Lakshminarasimhan |
E-mail(s) |
ranjanil@usc.edu
|
Phone |
3238650736
|
Organization name |
University of Southern California
|
Department |
Urology
|
Lab |
Jones/Liang
|
Street address |
1441 Eastlake ave NOR7336
|
City |
Los Angeles |
State/province |
California |
ZIP/Postal code |
90033 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE86810 |
Genome-wide histone modification profiling in endometriosis cells |
|
Relations |
BioSample |
SAMN05762547 |
SRA |
SRX2158975 |