|
| Status |
Public on Aug 20, 2015 |
| Title |
GM18858_H3K4ME3 |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoblastoid Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM18858
antibody: H3K4ME3
|
| Treatment protocol |
Cross linking was performed in 1% formaldehyde for 10 minutes at room temperature. Followed by quenching with Glycin with a final concentration of 125mM
|
| Growth protocol |
LCLs were grown to a density of 0.6-0.8 x 10^6/mL in RPMI1640 with 15% fetal bovine serum and 1% PenStrep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-Seq, nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals). Clarified lysates corresponding to 20 million cells were treated with 1-5ug of antibody coupled to Protein G Dynabeads (Invitrogen #10003D, New York). The protein-DNA complexes were washed with RIPA buffer and eluted in 1% SDS TE at 65°C.
ChIP DNA sequencing libraries were generated according to Illumina DNA Tru-Seq DNA Sample Preparation Kit Instructions (Illumina Part # FC-121-2001, San Diego, CA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Personal genomes were created by adding the SNPs of each individual into hg19. SNPs were obtained from the 1000 Genomes Project or imputed using shapeIt and IMPUTE2
ChIP-seq reads were aligned to personal genomes with BWA 0.6.1 (options -q 20, -t 4 and the rest set to defaults)
Peaks were called using MACS2 on merged replicates, subsampled to 50 million single reads. Genome-wide signal tracks (bigWig) were generated using wiggler, also on the subsampled data.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks are in the narrowPeak format. bigWig files were generated using wiggler.
|
| |
|
| Submission date |
Nov 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Fabian Grubert |
| E-mail(s) |
fabian.grubert@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE62742 |
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions |
|
| Relations |
| BioSample |
SAMN03202735 |
| SRA |
SRX764675 |
