|
| Status |
Public on Apr 05, 2017 |
| Title |
KD2_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
Endometriosis
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hTERT immortalized endometriosis cells
genotype/variation: ARID1A Knockdown
antibody: H3K4me3
|
| 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 NextSeq 500 |
| |
|
| 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 |
GPL18573 |
| Series (1) |
| GSE86810 |
Genome-wide histone modification profiling in endometriosis cells |
|
| Relations |
| BioSample |
SAMN05762545 |
| SRA |
SRX2158977 |
