|
| Status |
Public on Nov 03, 2014 |
| Title |
LCL19240_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoblastoid cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lymphoblastic cell line
chip antibody: H3K4me3 (Diagenode; #pAb-003-050)
|
| Growth protocol |
Lymphoblastic cell lines were cultured in RPMI 1640 medium supplemented with penicillin/streptomycin, 2 mM L-Glutamine and 15% heat-inactivated fetal bovine serum. The cells were grown at 37°C and 5% CO2. The cell growth was monitored using a hemocytometer and cultures were harvested at a density of 0.8–1.1×106 cells/ml. The cells were lyzed by resuspension in Trizol reagent.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to the Illumina TruSeq protocol, and quality assessed by Agilent 2100 BioAnalyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Trimmomatic v0.22 was used for trimming reads for quality (phred33>=30) and length (n>=32)
For ChIP-seq, filtered reads were aligned to hg19 using BWA v0.6.1.
Genome_build: hg19
|
| |
|
| Submission date |
Jul 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tony Kwan |
| E-mail(s) |
tony.kwan@mcgill.ca
|
| Phone |
514-398-3311
|
| Organization name |
McGill University
|
| Department |
Human Genetics
|
| Street address |
740 Dr. Penfield
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3A 0G1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE53837 |
Allelic expression mapping across cell lineages reveal repressor disruption among disease SNPs |
|
| Relations |
| BioSample |
SAMN02910204 |
| SRA |
SRX651494 |
