|
| Status |
Public on Nov 04, 2012 |
| Title |
WCE 25mM sodium bicarbonate |
| Sample type |
SRA |
| |
|
| Source name |
WCE 25mM sodium bicarbonate
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: none
agent: 25mM sodium bicarbonate
cell line: HeLa
|
| Treatment protocol |
Cells were plated in 10-cm dishes and allowed to attach overnight. The following day the culture medium was replaced with DMEM (Sigma #D5030 supplemented with glucose, glutamine and pyruvate) with either 25 mM or 3 mM sodium bicarbonate which resulted in a medium pH of 7.4 and 6.5, respectively. After 4 hours of incubation at 37oC in 5% CO2, cells were fixed with formaldehyde and harvested for ChIP.
|
| Growth protocol |
Cells were routinely cultured in DMEM (Cellgro) that was supplemented with 10% FBS (Hyclone) and 1X antibiotic/antimycotic (Gibco). Cells were passaged every 2-3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nugen Ovation Ultralow Library system
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
input pH 7.4 ChIP-seq
|
| Data processing |
bowtie alignment -m1 -5 4 --strata --best -v2
value < 1.0 E-4 was chosen to give False Discovery Rate (FDR) less than 1%. FDR was calculated by applying the same statistic, described above, to the two halves of the same input library. We considered the total number of significant peaks obtained this way as an estimate of number of false-positive peaks. To compare two ChIP samples to identify regions that are significantly different between the two samples (for instance e1a versus mock), we replaced the input sample with the sample used for comparison; all downstream analyses were identical. Our algorithm produces several files that were subsequently used for analysis: BED files containing the coordinates of the significant windows of enrichment; Wiggle (wig) files (chromosome tiling, fixed step) with normalized reads count for the significant windows (If a window was not significant, we placed zero tags); GR files of normalized raw counts for input and ChIP samples were also created for genome browser visualization. Tiling profiles of promoter regions for the hg19 annotated human promoters were also generated. These represent the 50-bp tiling of a 10 Kb region spanning the transcription start site (TSS). We reported the number of reads falling into significant windows and zero for the non-significant ones.
peak calling described in Ferrari et al. 2012 Genome Research
Genome_build: hg19
Supplementary_files_format_and_content: bed
|
| |
|
| Submission date |
Aug 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
Skurdistani@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Lab |
Kurdistani
|
| Street address |
615 Charles E Young Dr South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE40114 |
Histone acetylation regulates intracellular pH |
|
| Relations |
| SRA |
SRX176644 |
| BioSample |
SAMN01113276 |
