|
| Status |
Public on Jun 04, 2014 |
| Title |
HMEC_H3K4me3_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
HMEC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HMEC
chip antibody: H3K4me3 (#39160, Active Motif)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were purified (described for NOMe-Seq) after formaldehyde crosslinking, collected and resuspended in SDS Lysis buffer before sonication. Chromatin was sonicated to generate a majority of fragments between 200 and 600 bp. 10µg of each antibody was used per ChIP.
Libraries for ChIP-Seq were prepared by the USC Epigenome Center following Illumina protocols. The resulting libraries were sequenced on the Illumina HiSeq 2000 platform configured for 50bp single-end reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 8
processed data file: HMEC_ChromHMM.bed
|
| Data processing |
ChIP-seq reads were aligned to hg19 using bowtie v0.12.8 allowing up to 3 mismatches, discarding ambiguous and clonal reads. ChromHMM v1.03 was used to simultaneously partition the genomes of all four cell lines into 15 chromatin states which were collapsed into 9 distinct states manually annotated by comparison to the published ChromHMM model for HMEC cells.
NOMe-seq reads were aligned to hg19 using BSMAP_2.01 and counts of methylated residues vs total sequencing counts at GCH and WCG sites summarized using custom R scripts. NDRs were detected by a 100bp sliding window in 20bp increments chi-squared test of GCH methylation versus the genome background with a p-value cutoff of -log10(p)>15, significant windows overlapped and retained if a minimum 140bp in size.
Genome_build: hg19
Supplementary_files_format_and_content: NDR bed files contain the -log10 pvalue in the name field (4th column). ChromHMM bed files report Consolidated ChromHMM States. GCH/WCG tsv files contain coordinates of cytosines in GCH/WCG genomic contexts and methylation values per cell line in two columns - C is the count of methylated calls and cov is the sequencing coverage at each position
|
| |
|
| Submission date |
May 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Aaron Statham |
| E-mail(s) |
a.statham@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Cancer Department
|
| Lab |
Epigenetics Research Laboratory
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE57498 |
Comparison of nucleosome occupancy and chromatin states between normal and cancer cell lines |
|
| Relations |
| BioSample |
SAMN02768449 |
| SRA |
SRX539647 |
