 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 15, 2017 |
| Title |
MB468.H3K4me3.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MB468 cells, H3K4me3 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MB468
cell type: Breast cancer cell line
treatment: Control
chip antibody: H3K4me3 (Abcam, ab8580, lot GR1902371-1 and GR224370-1)
|
| Treatment protocol |
Cells are harvested from the 150mm plates under sterile conditions into a 50ml conical tube. Aliquots of 100-200ul of this stock are then counted using the Biorad Cell Counter. Counts are repeated three times and the number of cells per ml are then determined. For growth curves, the schema in the Powerpoint entitled “Growthcurveprotocol” is followed. Briefly, 500-5000 cells (for each cell line) were plated onto each well of a 96-well plate on day 0. For each cell line, a total of 7 replicate plates were seeded. The media was changed every other day (days 1, 3, 5, 7, 9, 11, and 13). One plate from each cell line was subjected to MTT proliferation assay every other day (days 1, 3, 5, 7, 9, 11, and 13).
|
| Growth protocol |
Cells were plated and expanded on 150mm plates until a minimum of 3.5 x 10^5 cells per plate were reached. The media conditions and split ratio for each cell line is depicted in the Excel sheet entitled “Cell line conditions”. Media is replaced every other day, until the desired confluency is reached.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed by Illumina CASAVA 1.8.2.
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6; Scores represent the ChIP-seq tag numbers.
|
| |
|
| Submission date |
Aug 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuanxin Xi |
| E-mail(s) |
xiyuanxin@yahoo.com
|
| Phone |
530-220-2067
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Bioinformatics and Computational Biology
|
| Street address |
1400 Pressler St
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE85158 |
Epigenetic Landscapes in Breast Cancer Cells |
|
| Relations |
| BioSample |
SAMN05509462 |
| SRA |
SRX1998139 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2258893_MB468.H3K4me3.rep2.wig.gz |
17.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
