|
| Status |
Public on Mar 15, 2016 |
| Title |
750N H3K4me3_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Patient x750 Adjacent Normal Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K4me3 (Active Motif, 39160)
tissue: Normal Kidney adjacent to tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Flash-frozen minced tissue was thawed in cell culture medium (Gibco® Keratinocyte-SFM (1X) Catalog #17005-042) with 1% formaldehyde for 10 minutes under rotation for cross-linking, which was then quenched with 2M Glycine (final concentration of 100mM). Minced tissue was then washed twice with ice-cold PBS with Protease Inhibitor Cocktail (PIC) and resuspended in 1mL ChIP Lysis Buffer (1% SDS, 50mM Tris HCl pH 8.1, 10mM EDTA) with PIC. The suspension was ground in a dounce homogenizer 10-15 times and then passed through a 40µM filter and checked for lysis with Trypan Blue under a microscope. The nuclei were then sonicated using a probe sonicator (Branson Sonifier® Cell Disruptor 185, 4.5 Output Control, 12 cycles, 10 seconds ON/30 seconds OFF) and centrifuged at 12,000rpm for 10 minutes at 4°C.
Libraries were constructed using the KAPA DNA library preparation kit (KK8230)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequencing reads were aligned to hg19 using BWA-0.6.2
Data were filtered by removing nonuniquely mapping reads and PCR duplicates
ChIP-seq reads were extended to sequencing library’s mean fragment size, estimated using the default setting of HOMER v.4.3’s makeTaqDirectory command
Each data set was normalized into a single value for each genomic position using the Wiggler tool with default settings and “globalmap_k20tok54” as the mappability parameter
Mean Wiggler values were calculated in 10-bp bins, and Z-score transformation by subtracting the mean Wiggler value across the genome and dividing by the standard deviation of the genome-wide Wiggler subtraction value
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigwig files were generated using the Wiggler tool; values represent Z-scores for each 10bp bin
|
| |
|
| Submission date |
Dec 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gangning Liang |
| E-mail(s) |
gliang@usc.edu
|
| Phone |
323-865-0470
|
| Organization name |
University of Southern California
|
| Department |
Urology
|
| Lab |
Gangning Liang Laboratory
|
| Street address |
1441 Eastlake Ave, NOR 7344
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE75597 |
Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma |
|
| Relations |
| BioSample |
SAMN04308767 |
| SRA |
SRX1458748 |
